Breast cancer progression signatures

ABSTRACT

Methods and compositions for the identification of breast cancer progression signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages of breast cancer.

FIELD OF THE INVENTION

The invention relates to the identification and use of gene expression profiles, or patterns, involved in breast cancer progression. The gene expression profiles, whether embodied in nucleic acid expression, protein expression, or other expression formats, are used in the study and/or diagnosis of cells and tissue during breast cancer progression as well as for the study and/or determination of prognosis of a patient. When used for diagnosis or prognosis, the profiles are used to predict the status and/or phenotype of cells and tissues relative to breast cancer and the treatment thereof.

BACKGROUND OF THE INVENTION

Breast cancer is by far the most common cancer among women. Each year, more than 180,000 and 1 million women in the U.S. and worldwide, respectively, are diagnosed with breast cancer. Breast cancer is the leading cause of death for women between ages 50-55, and is the most common non-preventable malignancy in women in the Western Hemisphere. An estimated 2,167,000 women in the United States are currently living with the disease (National Cancer Institute, Surveillance Epidemiology and End Results (NCI SEER) program, Cancer Statistics Review (CSR), www-seer.ims.nci.nih.gov/Publications/CSR1973 (1998)). Based on cancer rates from 1995 through 1997, a report from the National Cancer Institute (NCI) estimates that about 1 in 8 women in the United States (approximately 12.8 percent) will develop breast cancer during her lifetime (NCI's Surveillance, Epidemiology, and End Results Program (SEER) publication SEER Cancer Statistics Review 1973-1997). Breast cancer is the second most common form of cancer, after skin cancer, among women in the United States. An estimated 250,100 new cases of breast cancer are expected to be diagnosed in the United States in 2001. Of these, 192,200 new cases of more advanced (invasive) breast cancer are expected to occur among women (an increase of 5% over last year), 46,400 new cases of early stage (in situ) breast cancer are expected to occur among women (up 9% from last year), and about 1,500 new cases of breast cancer are expected to be diagnosed in men (Cancer Facts & Figures 2001 American Cancer Society). An estimated 40,600 deaths (40,300 women, 400 men) from breast cancer are expected in 2001. Breast cancer ranks second only to lung cancer among causes of cancer deaths in women. Nearly 86% of women who are diagnosed with breast cancer are likely to still be alive five years later, though 24% of them will die of breast cancer after 10 years, and nearly half (47%) will die of breast cancer after 20 years.

Every woman is at risk for breast cancer. Over 70 percent of breast cancers occur in women who have no identifiable risk factors other than age (U.S. General Accounting Office. Breast Cancer, 1971-1991: Prevention, Treatment and Research. GAO/PEMD-92-12; 1991). Only 5 to 10% of breast cancers are linked to a family history of breast cancer (Henderson IC, Breast Cancer. In: Murphy G P, Lawrence W L, Lenhard R E (eds). Clinical Oncology. Atlanta, Ga.: American Cancer Society; 1995:198-219).

Each breast has 15 to 20 sections called lobes. Within each lobe are many smaller lobules. Lobules end in dozens of tiny bulbs that can produce milk. The lobes, lobules, and bulbs are all linked by thin tubes called ducts. These ducts lead to the nipple in the center of a dark area of skin called the areola. Fat surrounds the lobules and ducts. There are no muscles in the breast, but muscles lie under each breast and cover the ribs. Each breast also contains blood vessels and lymph vessels. The lymph vessels carry colorless fluid called lymph, and lead to the lymph nodes. Clusters of lymph nodes are found near the breast in the axilla (under the arm), above the collarbone, and in the chest.

Breast tumors can be either benign or malignant. Benign tumors are not cancerous, they do not spread to other parts of the body, and are not a threat to life. They can usually be removed, and in most cases, do not come back. Malignant tumors are cancerous, and can invade and damage nearby tissues and organs. Malignant tumor cells may metastisize, entering the bloodstream or lymphatic system. When breast cancer cells metastisize outside the breast, they are often found in the lymph nodes under the arm (axillary lymph nodes). If the cancer has reached these nodes, it means that cancer cells may have spread to other lymph nodes or other organs, such as bones, liver, or lungs.

Major and intensive research has been focussed on early detection, treatment and prevention. This has included an emphasis on determining the presence of precancerous or cancerous ductal epithelial cells. These cells are analyzed, for example, for cell morphology, for protein markers, for nucleic acid markers, for chromosomal abnormalities, for biochemical markers, and for other characteristic changes that would signal the presence of cancerous or precancerous cells. This has led to various molecular alterations that have been reported in breast cancer, few of which have been well characterized in human clinical breast specimens. Molecular alterations include presence/absence of estrogen and progesterone steroid receptors, HER-2 expression/amplification (Mark H F, et al. HER-2/neu gene amplification in stages I-IV breast cancer detected by fluorescent in situ hybridization. Genet Med; 1(3):98-103 1999), Ki-67 (an antigen that is present in all stages of the cell cycle except G0 and used as a marker for tumor cell proliferation, and prognostic markers (including oncogenes, tumor suppressor genes, and angiogenesis markers) like p53, p27, Cathepsin D, pS2, multi-drug resistance (MDR) gene, and CD31.

Examination of cells by a trained pathologist has also been used to establish whether ductal epithelial cells are normal (i.e. not precancerous or cancerous or having another noncancerous abnormality), precancerous (i.e. comprising hyperplasia, atypical ductal hyperplasia (ADH)) or cancerous (comprising ductal carcinoma in situ, or DCIS, which includes low grade ductal carcinoma in situ, or LG-DCIS, and high grade ductal carcinoma in situ, or HG-DCIS) or invasive (ductal) carcinoma (IDC). Pathologists may also identify the occurrence of lobular carcinoma in situ (LCIS) or invasive lobular carcinoma (ILC). Breast cancer progression may be viewed as the occurrence of abnormal cells, such as those of ADH, DCIS, IDC, LCIS, and/or ILC, among normal cells.

It remains unclear whether normal cells become hyperplastic (such as ADH) and then progressing on to become malignant (DCIS, IDC, LCIS, and/or ILC) or whether normal cells are able to directly become malignant without transitioning through a hyperplastic stage. It has been observed, however, that the presence of ADH indicates a higher likelihood of developing a malignancy. This has resulting in treatment of patients with ADH to begin treatment with an antineoplastic/antitumor agent such as tamoxifen. This is in contrast to the treatment of patients with malignant breast cancer which usually includes surgical removal.

The rational development of preventive, diagnostic and therapeutic strategies for women at risk for breast cancer would be aided by a molecular map of the tumorigenesis process. Relatively little is known of the molecular events that mediate the transition of normal breast cells to the various stages of breast cancer progression. In particular, there is a significant paucity of information regarding the genetic changes that are associated with the earliest stages of human breast cancer, which include the transition of normal breast cells to atypical hyperplastic and/or pre-invasive malignant cells (carcinoma in situ).

Molecular means of identifying the differences between normal, non-cancerous cells and cancerous cells (in general) have also been the focus of intense study. The use of cDNA libraries to analyze differences in gene expression patterns in normal versus tumorigenic cells has been described (U.S. Pat. No. 4,981,783). DeRisi et al. (1996) describe the analysis of gene expression patterns between two cell lines: UACC-903, which is a tumorigenic human melanoma cell line, and UACC-903(+6), which is a chromosome 6 suppressed non-tumorigenic form of UACC-903. Labeled cDNA probes made from mRNA from these cell lines were applied to DNA microarrays containing 870 different cDNAs and controls. Genes that were preferentially expressed in one of the two cell lines were identified.

Golub et al. (1999) describe the use of gene expression monitoring as means to cancer class discovery and class prediction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Their approach to class predictors used a neighborhood analysis followed by cross-validation of the validity of the predictors by withholding one sample and building a predictor based only on the remaining samples. This predictor is then used to predict the class of the withheld sample. They also used cluster analysis to identify new classes (or subtypes) within the AML and ALL.

Gene expression patterns in human breast cancers have been described by Perou et al. (1999), who studied gene expression between cultured human mammary epithelia cells (HMEC) and breast tissue samples by use of microarrays comprising about 5000 genes. They used a clustering algorithm to identify patterns of expression in HMEC and tissue samples. Perou et al. (2000) describe the use of clustered gene expression profiles to classify subtypes of human breast tumors. Hedenfalk et al. describe gene expression profiles in BRCA1 mutation positive, BRCA2 mutation positive, and sporadic tumors. Sgroi et al. also analyzed gene expression of normal and breast cancer cells from a single patient. Using gene expression patterns to distinguish breast tumor subclasses and predict clinical implications is described by Sorlie et al. and West et al.

All of the above described approaches, however, utilize heterogeneous populations of cells found in culture or in a biopsy to obtain information on gene expression patterns. The use of such populations may result in the inclusion or exclusion of multiple genes from the patterns. For this and the lack of statistical robustness reasons, the gene expression patterns observed by the above described approaches provide little confidence that the differences in gene expression may be meaningfully associated with the stages of breast cancer.

SUMMARY OF THE INVENTION

The present invention relates to the identification and use of gene expression patterns (or profiles or “signatures”) which are correlated with (and thus able to discriminate between) cells in various stages of breast cancer. Broadly defined, these stages are non-malignant versus malignant, but may also be viewed as normal versus atypical (optionally including reactive and pre-neoplastic) versus cancerous. Another definition of the stages is normal versus precancerous (e.g. atypical ductal hyperplasia (ADH) or atypical lobular hyperplasia (ALH)) versus cancerous (e.g. carcinoma in situ such as DCIS and/or LCIS) versus invasive (e.g. carcinomas such as IDC and/or ILC). DCIS may be further viewed as low grade versus high grade or grade I through grade III.

The gene expression patterns comprise one or more than one gene capable of discriminating between various stages of breast cancer with significant accuracy. The gene(s) are identified as correlated with various stages of breast cancer such that the levels of their expression are relevant to a determination of the stage of breast cancer of a cell. Thus in one aspect, the invention provides a method to determine the stage of breast cancer of a subject afflicted with, or suspected of having, breast cancer by assaying a cell containing sample from said subject for expression of one or more than one gene disclosed herein as correlated with one or more stages of breast cancer.

Gene expression patterns of the invention are identified by analysis of gene expression in multiple samples of each stage to be studied. The overall gene expression profile of each sample is obtained by analyzing the expressed or unexpressed state of genes in each stage relative to each other (one gene to another across all genes). This overall profile is then analyzed to identify genes that are positively, or negatively, correlated, with a stage of breast cancer relative to other genes. An expression profile of a subset of human genes may then be identified by the methods of the present invention as correlated with breast cancer. The use of multiple samples increases the confidence which which a gene may be believed to be correlated with a particular stage. Without sufficient confidence, it remains unpredictable whether a particular gene is actually correlated with a stage of breast cancer and also unpredictable whether a particular gene may be successfully used to identify the stage of an unknown breast cancer cell sample.

A profile of genes that are highly correlated with one stage relative to another may be used to assay an sample from a subject afflicted with, or suspected of having, breast cancer to identify the stage of breast cancer to which the sample belongs. Such an assay may be used as part of a method to determine the therapeutic treatment for said subject based upon the stage(s) of breast cancer identified.

The correlated genes may be used singly with significant accuracy or in combination to increase the ability to accurately discriminate between various stages of breast cancer. The present invention thus provides means for correlating a molecular expression phenotype with a physiological (cellular) stage or state. This correlation provides a way to molecularly diagnose and/or monitor a cell's status in comparison to different cancerous versus non-cancerous phenotypes as disclosed herein. Additional uses of the correlated gene(s) are in the classification of cells and tissues; determination of diagnosis and/or prognosis; and determination and/or alteration of therapy.

The ability to discriminate is conferred by the identification of expression of the individual genes as relevant and not by the form of the assay used to determine the actual level of expression. An assay may utilize any identifying feature of an identified individual gene as disclosed herein as long as the assay reflects, quantitatively or qualitatively, expression of the gene. Identifying features include, but are not limited to, unique nucleic acid sequences used to encode (DNA), or express (RNA), said gene or epitopes specific to, or activities of, a protein encoded by said gene. All that is required is the identity of the gene(s) necessary to discriminate between stages of breast cancer and an appropriate cell containing sample for use in an expression assay.

In one aspect, the invention provides for the identification of the gene expression patterns by analyzing global, or near global, gene expression from single cells or homogenous cell populations which have been dissected away from, or otherwise isolated or purified from, contaminating cells beyond that possible by a simple biopsy. Because the expression of numerous genes fluctuate between cells from different patients as well as between cells from the same patient sample, multiple individual gene expression patterns are used as reference data to generate models which in turn permit the identification of individual gene(s) that are most highly correlated with particular breast cancer stages and/or have the best the ability to discriminate cells of one stage from another.

In another aspect, the invention provides physical and methodological means for detecting the expression of gene(s) identified by the models generated by individual expression patterns. These means may be directed to assaying one or more aspect of the DNA template(s) underlying the expression of the gene(s), of the RNA used as an intermediate to express the gene(s), or of the proteinaceous product expressed by the gene(s).

In a further aspect, the gene(s) identified by a model as capable of discriminating between breast cancer stages may be used to identify the cellular state of an unknown sample of cell(s) from the breast. Preferably, the sample is isolated via non-invasive means. The expression of said gene(s) in said unknown sample may be determined and compared to the expression of said gene(s) in reference data of gene expression patterns from the various stages of breast cancer. Optionally, the comparison to reference samples may be by comparison to the model(s) constructed based on the reference samples.

One advantage provided by the present invention is that contaminating, non-breast cells (such as infiltrating lymphocytes or other immune system cells) are not present to possibly affect the genes identified or the subsequent analysis of gene expression to identify the status of suspected breast cancer cells. Such contamination is present where a biopsy is used to generate gene expression profiles.

While the present invention has been described mainly in the context of human breast cancer, it may be practiced in the context of breast cancer of any animal known to be potentially afflicted by breast cancer. Preferred animals for the application of the present invention are mammals, particularly those important to agricultural applications (such as, but not limited to, cattle, sheep, horses, and other “farm animals”) and for human companionship (such as, but not limited to, dogs and cats).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic representing a data matrix of a pair-wise comparison between Grade I and Grade III DCIS among 16 samples (across the top) and a large number of genes identified by “CloneID”) along the left hand side.

FIG. 2 is a table showing the actual weight data corresponding to Example II, where the data from ten genes (by CloneID number vertically) are compared to DCIS and ADH samples (across the top). Some data in the table has been vertically presented to permit the table to be displayed on a single sheet. The use of “−” with data in the table reflects genes that are more highly expressed in ADH relative to DCIS. The absence of “−”reflects genes that are more highly expressed in DCIS relative to ADH.

FIG. 3 is a table showing the actual weight data corresponding to Example VII, where the data from over 300 genes (by CloneID number vertically) are compared to DCIS and ADH samples (across the top). Some data in the table has been vertically presented solely for display purposes. The use of “−” with data in the table reflects genes that are more highly expressed in ADH relative to DCIS. The absence of “−” reflects genes that are more highly expressed in DCIS relative to ADH.

FIG. 4 is a table showing the actual weight data corresponding to Example VIII, where the data from over 300 genes (by CloneID number vertically) are compared to samples (across the top) from two grades of DCIS. The use of “−” with data in the table reflects genes that are more highly expressed in grade I relative to grade III. The absence of “−” reflects genes that are more highly expressed in grade III relative to grade I.

DETAILED DESCRIPTION OF THE SPECIFIC EMBODIMENTS

Definitions of Terms as used Herein:

A gene expression “pattern” or “profile” or “signature” refers to the relative expression of a gene between two or more stages of breast cancer which is correlated with being able to distinguish between said stages.

A “gene” is a polynucleotide that encodes a discrete product, whether RNA or proteinaceous in nature. It is appreciated that more than one polynucleotide may be capable of encoding a discrete product. The term includes alleles and polymorphisms of a gene that encodes the same product, or a functionally associated (including gain, loss, or modulation of function) analog thereof, based upon chromosomal location and ability to recombine during normal mitosis.

A “stage” or “stages” (or equivalents thereof) of breast cancer refer to a physiologic state of a breast cell as defined by known cytological or histological (including immunohistology, histochemistry, and immunohistochemistry) procedures and are readily known to skilled in the art. Non-limiting examples include normal versus abnormal, non-cancerous versus cancerous, the different stages described herein (e.g. hyperplastic, carcinoma, and invasive), and grades within different stages (e.g. grades I, II, or III or the equivalents thereof within cancerous stages).

The terms “correlate” or “correlation” or equivalents thereof refer to an association between expression of one or more genes and a physiologic state of a breast cell to the exclusion of one or more other stages and/or identified by use of the methods as described herein. A gene may be expressed at higher or lower levels and still be correlated with one or more breast cancer stages.

A “polynucleotide” is a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA and RNA. It also includes known types of modifications including labels known in the art, methylation, “caps”, substitution of one or more of the naturally occurring nucleotides with an analog, and internucleotide modifications such as uncharged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), as well as unmodified forms of the polynucleotide.

The term “amplify” is used in the broad sense to mean creating an amplification product can be made enzymatically with DNA or RNA polymerases. “Amplification,” as used herein, generally refers to the process of producing multiple copies of a desired sequence, particularly those of a sample. “Multiple copies” mean at least 2 copies. A “copy” does not necessarily mean perfect sequence complementarity or identity to the template sequence.

By corresponding is meant that a nucleic acid molecule shares a substantial amount of sequence identity with another nucleic acid molecule. Substantial amount means at least 95%, usually at least 98% and more usually at least 99%, and sequence identity is determined using the BLAST algorithm, as described in Altschul et al. (1990), J. Mol. Biol. 215:403-410 (using the published default setting, i.e. parameters w=4, t=17). Methods for amplifying mRNA are generally known in the art, and include reverse transcription PCR (RT-PCR) and those described in U.S. Patent Application (number to be assigned) entitled “Nucleic Acid Amplification” filed on Oct. 25, 2001 as attorney docket number 485772002900 as well as U.S. Provisional Patent Application 60/298,847 (filed Jun. 15, 2001) and 60/257,801 (filed Dec. 22, 2000), all of which are hereby incorporated by reference in their entireties as if fully set forth. Alternatively, RNA may be directly labeled as the corresponding cDNA by methods known in the art.

A “microarray” is a linear or two-dimensional array of preferably discrete regions, each having a defined area, formed on the surface of a solid support such as, but not limited to, glass, plastic, or synthetic membrane. The density of the discrete regions on a microarray is determined by the total numbers of immobilized polynucleotides to be detected on the surface of a single solid phase support, preferably at least about 50/cm², more preferably at least about 100/cm², even more preferably at least about 500/cm², but preferably below about 1,000/cm². Preferably, the arrays contain less than about 500, about 1000, about 1500, about 2000, about 2500, or about 3000 immobilized polynucleotides in total. As used herein, a DNA microarray is an array of oligonucleotides or polynucleotides placed on a chip or other surfaces used to hybridize to amplified or cloned polynucleotides from a sample. Since the position of each particular group of primers in the array is known, the identities of a sample polynucleotides can be determined based on their binding to a particular position in the microarray.

Because the invention relies upon the identification of genes that are over- or under-expressed, one embodiment of the invention involves determining expression by hybridization of mRNA, or an amplified or cloned version thereof, of a sample cell to a polynucleotide that is unique to a particular gene sequence. Preferred polynucleotides of this type contain at least about 20, at least about 22, at least about 24, at least about 26, at least about 28, at least about 30, or at least about 32 consecutive basepairs of a gene sequence that is not found in other gene sequences. The term “about” as used in the previous sentence refers to an increase or decrease of 1 from the stated numerical value. Even more preferred are polynucleotides of at least about 50, at least about 100, and at least about 150 basepairs of a gene sequence that is not found in other gene sequences. The term “about” as used in the preceding sentence refers to an increase or decrease of 10% from the stated numerical value.

Alternatively, and in another embodiment of the invention, gene expression may be determined by analysis of expressed protein in a cell sample of interest by use of one or more antibodies specific for one or more epitopes of individual gene products (proteins) in said cell sample. Such antibodies are preferably labeled to permit their easy detection after binding to the gene product.

The term “label” refers to a composition capable of producing a detectable signal indicative of the presence of the labeled molecule. Suitable labels include radioisotopes, nucleotide chromophores, enzymes, substrates, fluorescent molecules, chemiluminescent moieties, magnetic particles, bioluminescent moieties, and the like. As such, a label is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.

The term “support” refers to conventional supports such as beads, particles, dipsticks, fibers, filters, membranes and silane or silicate supports such as glass slides.

As used herein, a “breast tissue sample” or “breast cell sample” refers to a sample of breast tissue or fluid isolated from an individual suspected of being afflicted with, or at risk of developing, breast cancer. Such samples are primary isolates (in contrast to cultured cells) and may be collected by any non-invasive means, including, but not limited to, ductal lavage, fine needle aspiration, needle biopsy, the devices and methods described in U.S. Pat. No. 6,328,709, or any other suitable means recognized in the art. Alternatively, the “sample” may be collected by an invasive method, including, but not limited to, surgical biopsy.

“Expression” and “gene expression” include transcription and/or translation of nucleic acid material.

As used herein, the term “comprising” and its cognates are used in their inclusive sense; that is, equivalent to the term “including” and its corresponding cognates.

Conditions that “allow” an event to occur or conditions that are “suitable” for an event to occur, such as hybridization, strand extension, and the like, or “suitable” conditions are conditions that do not prevent such events from occurring. Thus, these conditions permit, enhance, facilitate, and/or are conducive to the event. Such conditions, known in the art and described herein, depend upon, for example, the nature of the nucleotide sequence, temperature, and buffer conditions. These conditions also depend on what event is desired, such as hybridization, cleavage, strand extension or transcription.

Sequence “mutation,” as used herein, refers to any sequence alteration in the sequence of a gene disclosed herein interest in comparison to a reference sequence. A sequence mutation includes single nucleotide changes, or alterations of more than one nucleotide in a sequence, due to mechanisms such as substitution, deletion or insertion. Single nucleotide polymorphism (SNP) is also a sequence mutation as used herein. Because the present invention is based on the relative level of gene expression, mutations in non-coding regions of genes as disclosed herein may also be assayed in the practice of the invention.

“Detection” includes any means of detecting, including direct and indirect detection of gene expression and changes therein. For example, “detectably less” products may be observed directly or indirectly, and the term indicates any reduction (including the absence of detectable signal). Similarly, “detectably more” product means any increase, whether observed directly or indirectly.

Unless defined otherwise all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs.

Specific Embodiments

The present invention relates to the identification and use of gene expression patterns (or profiles or “signatures”) which discriminate between (or are correlated with) cells in various stages of breast cancer. Such patterns may be determined by the methods of the invention by use of a number of reference cell or tissue samples, such as those reviewed by a pathologist of ordinary skill in the pathology of breast cancer, which reflect various stages of breast cancer. Because the overall gene expression profile differs from person to person, cancer to cancer, and cancer cell to cancer cell, correlations between certain cell states and genes expressed or underexpressed may be made as disclosed herein to identify genes that are capable of discriminating between different breast cancer states.

The present invention may be practiced with any number of genes believed, or likely to be, differentially expressed in breast cancer cells. In Example I below, approximately 12,000 genes were used to identify hundreds of genes capable of discriminating between various stages of breast cancer as shown in Examples 2-9. The identification may be made by using expression profiles of various homogenous normal and breast cancer cell populations, which were isolated by microdissection, such as, but not limited to, laser capture microdissection (LCM) of 100-1000 cells. Each gene of the expression profile may be assigned weights based on its ability to discriminate between two or more stages of breast cancer (see Example I). The magnitude of each assigned weight indicates the extent of difference in expression between the two groups and is an approximation of the ability of expression of the gene to discriminate between the two groups (and thus stages). The magnitude of each assigned weight also approximates the extent of correlation between expression of individual gene(s) and particular breast cancer stages.

It should be noted that merely high levels of expression in cells from a particular stage or stages does not necessarily mean that a gene will be identified as having a high absolute weight value.

Genes with top ranking weights (in absolute terms) may be used to generate models of gene expressions that would maximally discriminate between the two groups. Alternatively, genes with top ranking weights (in absolute terms) may be used in combination with genes with lower weights without signficant loss of ability to discriminate between groups. Such models may be generated by any appropriate means recognized in the art, including, but not limited to, cluster analysis, supported vector machines, neural networks or other algorithm known in the art. The models are capable of predicting the classification of a unknown sample based upon the expression of the genes used for discrimination in the models. “Leave one out” cross-validation may be used to test the performance of various models and to help identify weights (genes) that are uninformative or detrimental to the predictive ability of the models. Cross-validation may also be used to identify genes that enhance the predictive ability of the models.

The gene(s) identified as correlated with particular breast cancer stages by the above models provide the ability to focus gene expression analysis to only those genes that contribute to the ability to identify a cell as being in a particular stage of breast cancer relative to another stage or stages. The expression of other genes in a breast cancer cell would be relatively unable to provide information concerning, and thus assist in the discrimination of, different stages of breast cancer. For example, the alpha subunit of human topoisomerase II (identified by CloneID 825470) has been found to be useful in discriminations between normal and atypical cells (ADH and DCIS and IDC and LCIS), between normal and ADH cells compared to DCIS and IDC cells, between normal and DCIS cells, between ADH and DCIS cells, between grade I and grade III DCIS cells, and between grade I and grade III IDC cells but not between normal and ADH cells (see Examples II to IX below). Thus expression of this topoisomerase II subunit would be utilized in models to discriminate between the above listed stages but not for discerning normal from ADH cells. This type of analysis is readily incorporated into algorithms used to generate models with reference gene expression data.

As will be appreciated by those skilled in the art, the models are highly useful with even a small set of reference gene expression data and can become increasingly accurate with the inclusion of more reference data although the incremental increase in accuracy will likely diminish with each additional datum. The preparation of additional reference gene expression data using genes identified and disclosed herein for discriminating between different stages of breast cancer is routine and may be readily performed by the skilled artisan to permit the generation of models as described above to predict the status of an unknown sample based upon the expression levels of those genes.

To determine the expression levels of genes in the practice of the present invention, any method known in the art may be utilized. In one preferred embodiment of the invention, expression based on detection of RNA which hybridizes to the genes identified and disclosed herein is used. This is readily performed by any RNA detection or amplification+detection method known or recognized as equivalent in the art such as, but not limited to, reverse transcription-PCR, the methods disclosed in U.S. Patent Application (number to be assigned) entitled “Nucleic Acid Amplification” filed on Oct. 25, 2001 as attorney docket number 485772002900 as well as U.S. Provisional Patent Applications 60/298,847 (filed Jun. 15, 2001) and 60/257,801 (filed Dec. 22, 2000), and methods to detect the presence, or absence, of RNA stabilizing or destabilizing sequences.

Alternatively, expression based on detection of DNA status may be used. Detection of the DNA of an indentified gene as methylated or deleted may be used for genes that have decreased expression in correlation with a particular breast cancer stage. This may be readily performed by PCR based methods known in the art. Conversely, detection of the DNA of an indentified gene as amplified may be used for genes that have increased expression in correlation with a particular breast cancer stage. This may be readily performed by PCR based, fluorescent in situ hybridization (FISH) and chromosome in situ hybridization (CISH) methods known in the art.

Expression based on detection of a presence, increase, or decrease in protein levels or activity may also be used. Detection may be performed by any immunohistochemistry (IHC) based, blood based (especially for secreted proteins), antibody (including autoantibodies against the protein) based, ex foliate cell (from the cancer) based, mass spectroscopy based, and image (including used of labeled ligand) based method known in the art and recognized as appropriate for the detection of the protein. Antibody and image based methods are additionally useful for the localization of tumors after determination of cancer by use of cells obtained by a non-invasive procedure (such as ductal lavage or fine needle aspiration), where the source of the cancerous cells is not known. A labeled antibody or ligand may be used to localize the carcinoma(s) within a patient.

A preferred embodiment using a nucleic acid based assay to determine expression is by immobilization of one or more of the genes identified herein on a solid support, including, but not limited to, a solid substrate as an array or to beads or bead based technology as known in the art. Alternatively, solution based expression assays known in the art may also be used. The immobilized gene(s) may be in the form of polynucleotides that are unique or otherwise specific to the gene(s) such that the polynucleotide would be capable of hybridizing to a DNA or RNA corresponding to the gene(s). These polynucleotides may be the full length of the gene(s) or be short sequences of the genes that are optionally minimally interrupted (such as by mismatches or inserted non-complementary basespairs) such that hybridization with a DNA or RNA corresponding to the gene(s) is not affected.

The immobilized gene(s) may be used to determine the state of nucleic acid samples prepared from sample breast cell(s) for which the pre-cancer or cancer status is not known or for confirmation of a status that is already assigned to the sample breast cell(s). Without limiting the invention, such a cell may be from a patient suspected of being afflicted with, or at risk of developing, breast cancer. The immobilized polynucleotide(s) need only be sufficient to specifically hybridize to the corresponding nucleic acid molecules derived from the sample. While even a single correlated gene sequence may to able to provide adequate accuracy in discriminating between two breast cancer cell stages, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, or eleven or more of the genes identified herein may be used as a subset capable of discriminating may be used in combination to increase the accuracy of the method. The invention specifically contemplates the selection of more than one, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, or eleven or more of the genes disclosed in the tables and figures herein for use as a subset in the identification of whether an unknown or suspicious breast cancer sample is normal or is in one or more stages of breast cancer. Optionally, the genes used will not include CloneID 809507, which is also known as GenBank accession number AA454563, described as an EST with high similarity to CD63 but of unknown function.

In embodiments where only one or a few genes are to be analyzed, the nucleic acid derived from the sample breast cancer cell(s) may be preferentially amplified by use of appropriate primers such that only the genes to be analyzed are amplified to reduce contaminating background signals from other genes expressed in the breast cell. Alternatively, and where multiple genes are to be analyzed or where very few cells (or one cell) is used, the nucleic acid from the sample may be globally amplified before hybridization to the immobilized polynucleotides. Of course RNA, or the cDNA counterpart thereof may be directly labeled and used, without amplification, by methods known in the art.

The above assay embodiments may be used in a number of different ways to identify or detect the breast cancer stage, if any, of a breast cancer cell sample from a patient. In many cases, this would reflect a secondary screen for the patient, who may have already undergone mammography or physical exam as a primary screen. If positive, the subsequent needle biopsy, ductal lavage, fine needle aspiration, or other analogous methods may provide the sample for use in the above assay embodiments. The present invention is particularly useful in combination with non-invasive protocols, such as ductal lavage or fine needle aspiration, to prepare a breast cell sample. The current analysis of ductal lavage samples is by cytological examination by a trained pathologist who classifies the samples in terms that are at least partly subjective: unsatisfactory (too few cells), benign (including fibrocystic change), atypical (or mild atypia), suspicious (or marked atypia), or malignant.

The present invention provides a more objective set of criteria, in the form of gene expression profiles of a discrete set of genes, to discriminate (or delineate) between meaningful stages (or classes) of breast cancer cells. In particularly preferred embodiments of the invention, the assays are used to discriminate between ADH and DCIS or otherwise malignant cells, which is a critical determination for decisions concerning subsequent treatment and therapy for the patient. Another particularly preferred determination is between the three grades (I, II, III) of carcinomas in situ as well as the discrimination between grade III carcinomas in situ and invasive carcinomas. Other pairwise comparisons that are provided by the invention include, but are not limited to, normal versus ADH, normal versus carcinoma in situ, normal versus invasive, normal versus cancerous (i.e. carcinoma present), ADH versus cancerous, and carcinoma in situ versus invasive. With the use of alternative algorithms, such as neural networks, comparisons that discriminate between multiple (more than pairwise) classes may also be performed. It is believed by the inventors that the present invention is the first example of objective, molecular criteria for making these discriminations.

In one embodiment of the invention, the isolation and analysis of a breast cancer cell sample may be performed as follows:

-   -   (1) Ductal lavage or other non-invasive procedure is performed         on a patient to obtain a sample.     -   (2) Sample is prepared and coated onto a microscope slide. Note         that ductal lavage results in clusters of cells that are         cytologically examined as stated above.     -   (3) Pathologist or image analysis software scans the sample for         the presence of atypical cells.     -   (4) If atypical cells are observed, those cells are harvested         (e.g. by microdissection such as LCM).     -   (5) RNA is extracted from the harvested cells.     -   (6) RNA is purified, amplified, and labeled.     -   (7) Labeled nucleic acid is contacted with a microarray         containing polynucleotides of the genes identified herein as         correlated to discriminations between two or more stages of         breast cancer under hybridization conditions, then processed and         scanned to obtain a pattern of intensities of each spot         (relative to a control for general gene expression in cells)         which determine the level of expression of the gene(s) in the         cells.     -   (8) The pattern of intensities is analyzed by comparison to the         expression patterns of the genes in known samples of normal and         breast cancer cells (relative to the same control).

A specific example of the above method would be performing ductal lavage following a primary screen, observing and collecting atypical cells for analysis. The comparison to known expression patterns, such as that made possible by a model generated by an algorithm (such as, but not limited to nearest neighbor type analysis, SVM, or neural networks) with reference gene expression data for the different breast cancer stages, identifies the cells as being most likely ADH.

Alternatively, the sample may permit the collection of both normal and atypical cells for analysis. The gene expression patterns for each of these two samples will be compared to each other as well as the model and the normal versus individual abnormal comparisons therein based upon the reference data set. This approach can be significantly more powerful that the atypical cells only approach because it utilizes significantly more information from the normal cells and the differences between normal and atypical cells (in both the sample and reference data sets) to determine the status of the atypical cells from the sample.

By appropriate selection of the genes used in the analysis, identification of the relative amounts of atypical cells may also be possible, although in most clinical settings, the identification of the highest grade of breast cancer with confidence makes identification of lower grades less important. Stated differently, the identification of invasive cancer determines the clinical situation regardless of the presence of carcinoma in situ or hyperplastic cells, or the identification of carcinoma in situ makes determines the clinical situation regardless of the presence of hyperplastic cells.

With use of the present invention, skilled physicians may prescribe treatments based on non-invasive samples that they would have prescribed for a patient which had previously received a diagnosis via a solid tissue biopsy.

The above discussion is also applicable where a palpable lesion is detected followed by fine needle aspiration or needle biopsy of cells from the breast. The cells are plated and reviewed by a pathologist or automated imaging system which selects cells for analysis as described above. This again provides a means of linking visual to molecular cytology and provides a less subjective means of identifying the physiological state of breast cancer cells without the need for invasive solid tissue biopsies.

The present invention may also be used, however, with solid tissue biopsies. For example, a solid biopsy may be collected and prepared for visualization followed by determination of expression of one or more genes identified herein to determine the stage of breast cancer, if any. One preferred means is by use of in situ hybridization with polynucleotide or protein identifying probe(s) for assaying expression of said gene(s).

In an alternative method, the solid tissue biopsy may be used to extract molecules followed by analysis for expression of one or more gene(s). This provides the possibility of leaving out the need for visualization and collection of only those cells suspected of being atypical. This method may of course be modified such that only cells suspected of being atypical are collected and used to extract molecules for analysis. This would require visualization and selection as an prerequisite to gene expression analysis.

In a further modification of the above, both normal cells and cells suspected of being atypical are collected and used to extract molecules for analysis of gene expression. The approach, benefits and results are as described above using non-invasive sampling.

In a further alternative to all of the above, the gene(s) identified herein may be used as part of a simple PCR or array based assay simply to determine the presence of atypical cells in a sample from a non-invasive sampling procedure. This is simple to perform and utilizes genes identified to be the best discriminators of normal versus abnormal cells without the need for any cytological examination. If no atypical cells are identified, no cytological examination is necessary. If atypical cells are identified, cytological examination follows, and a more comprehensive analysis, as described above, may follow.

The genes identified herein may be used to generate a model capable of predicting the breast cancer stage (if any) of an unknown breast cell sample based on the expression of the identified genes in the sample. Such a model may be generated by any of the algorithms described herein or otherwise known in the art as well as those recognized as equivalent in the art using gene(s) (and subsets thereof) disclosed herein for the identification of whether an unknown or suspicious breast cancer sample is normal or is in one or more stages of breast cancer. The model provides a means for comparing expression profiles of gene(s) of the subset from the sample against the profiles of reference data used to build the model. The model can compare the sample profile against each of the reference profiles or against model defining delineations made based upon the reference profiles. Additionally, relative values from the sample profile may be used in comparison with the model or reference profiles.

In a preferred embodiment of the invention, breast cell samples identified as normal and abnormal (atypical) from the same subject may be analyzed for their expression profiles of the genes used to generate the model. This provides an advantageous means of identifying the stage of the abnormal sample based on relative differences from the expression profile of the normal sample. These differences can then be used in comparison to differences between normal and individual abnormal reference data which was also used to generate the model.

The detection of gene expression from the samples may be by use of a single microarray able to assay gene expression from all pairwise comparisons disclosed herein for convenience and accuracy.

Other uses of the present invention include providing the ability to identify breast cancer cell samples as being those of a particular stage of cancer for further research or study. This provides a particular advantage in many contexts requiring the identification of breast cancer stage based on objective genetic or molecular criteria rather than cytological observation. It is of particular utility to distinguish different grades of a particular breast cancer stage for further study, research or characterization because no objective criteria for such delineation was previously available.

The materials for use in the methods of the present invention are ideally suited for preparation of kits produced in accordance with well known procedures. The invention thus provides kits comprising agents for the detection of expression of the disclosed genes for identifying breast cancer stage. Such kits optionally comprising the agent with an identifying description or label or instructions relating to their use in the methods of the present invention, is provided. Such a kit may comprise containers, each with one or more of the various reagents (typically in concentrated form) utilized in the methods, including, for example, pre-fabricated microarrays, buffers, the appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP and dTTP; or rATP, rCTP, rGTP and UTP), reverse transcriptase, DNA polymerase, RNA polymerase, and one or more primer complexes of the present invention (e.g., appropriate length poly(T) or random primers linked to a promoter reactive with the RNA polymerase). A set of instructions will also typically be included.

The methods provided by the present invention may also be automated in whole or in part. All aspects of the present invention may also be practiced such that they consist essentially of a subset of the disclosed genes to the exclusion of material irrelevant to the identification of breast cancer stages in a cell containing sample.

Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified.

EXAMPLES Example I Materials and Methods

Clinical Specimens

Clinical biopsies from 30 patients were obtained from the Massachusetts General Hospital with Institutional Review Board approval. The tissue from one of the patients was not associated with breast cancer of any kind since it was from a breast reduction procedure. Pathological and histological information for the biopsies were also obtained. Three independent captures of about 1000 breast epithelial cells of one or more of the four different disease stages (normal, N; atypical ductal hyperplasia, ADH; ductal carcinoma in situ, DCIS; invasive ductal carcinoma, IDC) were procured from each biopsy using Laser Capture Microdissection (LCM, Arcturus Engineering). Three independent captures of LCIS (lobular carcinoma in situ) in one biopsy were also made. Total RNA was extracted from the captured (procured) cells and amplified with a T7-promoter based RNA amplification protocol. The human universal reference RNA (Stratagene, La Jolla), was similarly amplified and used as the reference channel in a two-color microarray hybridization.

Microarrays

To maximize coverage of breast cancer-related genes on the microarrays used, 11,435 cDNA clones from the IMAGE consortium (Research Genetics) were obtained. These clones were selected based on literature knowledge (such as, but not limited to, preferential expression in cancer versus normal cells) and after mining (such as, but not limited to, preferential expression in breast tissues) gene expression information in the expressed sequence tags (EST) databases and the Serial Analysis of Gene Expression (SAGE) data sets available from the National Center for Biotechnology Information (NCBI, http://www/ncbi.nlm.nih.gov).

Microarray Data Processing

Microarray images were analyzed with ImaGene (BioDiscovery) to find and quantitate each spot on the microarray. Spots flagged by ImaGene as poor spots using standard criteria used with the software for the standardization of signals were excluded from further analysis. Raw Cy5 (sample channel) and Cy3 (reference channel) intensities and associated local background estimates for each spot were then examined. The signal/noise ratio, defined as the spot intensity over background intensity, was used as the second criteria for spot exclusion; spots with signal/noise ratio<3.0 in the reference channel or <1.5 in the sample channel were excluded from further analysis. Background-subtracted intensities across the chip were normalized to the 75th-percentile of the spot intensity distribution on the entire chip (alternative normalizations to the mean, median or other point may also be used as known in the art). Cy5/Cy3 ratios of each spot for each cellular state were averaged across each of six measurements (3 LCM captures×2 chips/capture=6 chips); outliers among the 6 data points were removed before taking the average. The resulting data were formatted as a data matrix (samples along the top horizontal axis and gene identity along the vertical axis) for data mining (see FIG. 1 with data).

Microarray Data Analysis

Before further analysis, each value in a row (gene) of the gene expression matrix was divided by the median value for the row, and the resulting matrix log-transformed. Normalized, median-centered, and log-transformed, gene expression data matrix was loaded into GeneMaths software (Applied-Maths, Belgium). Clustering and discriminant analysis were performed to identify sets of genes associated with different cellular states. For each pair-wise comparison between two breast cancer stages, samples are assigned to either the positive group or negative group, and genes were sorted by their discriminatory weights. The absolute value of the weight of a gene indicates the extent of difference in expression between the two groups; the positively signed genes are expressed higher in one group and the negatively singed genes are expressed higher in the other group.

The utility of the top-ranking genes as a diagnostic test was evaluated using the support vector machines (SVMs) algorithm (see Yeang, C. H., S. Ramaswamy, et al. (2001). “Molecular classification of multiple tumor types.” Bioinformatics 17 Suppl 1: S316-22; Xiong, M., X. Fang, et al. (2001). “Biomarker identification by feature wrappers.” Genome Res 11 (11): 1878-87 this one used linear discriminate analysis, logistic regression and svm; Furey, T. S., N. Cristianini, et al. (2000). “Support vector machine classification and validation of cancer tissue samples using microarray expression data.” Bioinformatics 16(10): 906-14; and Brown, M. P., W. N. Grundy, et al. (2000). “Knowledge-based analysis of microarray gene expression data by using support vector machines.” Proc Natl Acad Sci USA 97(1): 262-7, who state “SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps.”) Other algorithms, such as, but not limited to, linear discriminate analysis, logistic regression, cluster analysis, K-th nearest neighbor, or neural nets.

The support vector machines algorithm finds the maximal margin hyperplane that separate the two groups under comparison. The method of leave-one-out cross-validation was used to test the performance of a given set of genes; one sample was taken in turn out of the training set and a model is built using the rest of the training set, which is in then applied to classify the left-out sample. The accuracy of the genes in the cross-validation procedure is the percentage of correct classifications over the total number of the training samples.

Example II 10 Genes for Discriminating Between ADH and DCIS

Based upon the methodology of Example I above, 10 genes identified as capable of discriminating between ADH and DCIS are listed in Table 1 below along with a brief description of the gene. CloneID as used in the context of the present invention refers to the IMAGE Consortium clone ID number of each gene, the sequences of which are hereby incorporated by reference in their entireties as they are available from the Consortium at http://image.llnl.gov/ as accessed on the filing date of the present application. Weight refers to the absolute value indicating the extent of difference in expression between ADH and DCIS where the positively signed values are expressed higher in ADH and the negatively signed values are expressed higher in DCIS; Chromosome Location refers to the human chromosome to which the gene has been assigned, and Description provides a brief identifier of what the gene encodes. The actual data corresponding to the assigned weights are shown in FIG. 2. TABLE 1 Chromosome GeneID Weight Location Description 825470 0.9946555 17q21-q22 topoisomerase (DNA) II alpha (170 kD) 595213 0.9884884 8 hypothetical protein 796694 0.9852686 17q25 baculoviral IAP repeat- containing 5 (survivin) 1404774 −1.5638738 12p12.1-p11.2 parathyroid hormone-like hormone 823871 −1.5260464 7 SPARC-like 1 (mast9, hevin) 1882697 −1.401878 17q22-q23 peanut (Drosophila)-like 2 140071 −1.3881954 2 frizzled-related protein 160192 −1.2551663 5 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens] 796542 −1.1401853 3q28 ets variant gene 5 (ets-related molecule) 611532 −1.1227597 11p15.5 troponin I, skeletal, fast

Examples III Genes for Discriminating Between Normal and Non-Normal (a Combination of ADH, DCIS, and IDC) Cells from Breast Tissue

As shown in Table 2 below, 850 genes were identified as being able to discriminate between normal and “abnormal” (defined in this instance as any sample that was not normal), which includes ADH, DCIS and IDC. TABLE 2 CloneID Weight Description 1323448 1.5470535 cysteine-rich protein 1 (intestinal) 788654 1.4818381 growth factor receptor-bound protein 2 35147 1.3764654 “ESTs, Weakly similar to unnamed protein product [H. sapiens]” 745606 1.3470375 hypothetical protein PP591 1500000 1.3204029 “H2B histone family, member B” 595037 1.3057353 retinoic acid induced 3 565319 1.2369212 Homo sapiens mRNA; cDNA DKFZp564B1264 (from clone DKFZp564B1264) 122077 1.2356703 putative membrane protein 1609836 1.2349106 glutamate-ammonia ligase (glutamine synthase) 1505038 1.2292506 hypothetical protein FLJ20171 178805 1.2225746 “Human DNA sequence from clone RP5-850E9 on chromosome 20. Contains part of the gene for a novel C2H2 type zinc finger protein similar to DrosophilaScratch (Scrt), Slug and Xenopus Snail, a novel gene similar to Drosophila CG6762, STSs, GSSs and five CpG 812238 1.2132886 hypothetical protein MGC4692 1492238 1.1991653 HSPC003 protein 366132 1.1911439 “succinate dehydrogenase complex, subunit C, integral membrane protein, 15 kD” 796469 1.1850928 HSPC150 protein similar to ubiquitin-conjugating enzyme 488964 1.1545223 “H2A histone family, member O” 471568 1.1466811 hematological and neurological expressed 1 1554549 1.1440029 hydroxyacyl glutathione hydrolase 283919 1.118257 “H2A histone family, member L” 1492463 1.087152 “selenoprotein X, 1” 199403 1.082569 “lectin, galactoside-binding, soluble, 8 (galectin 8)” 796723 1.0724133 Homo sapiens clone CDABP0014 mRNA sequence 138189 1.0692241 Wolfram syndrome 1 (wolframin) 1574058 1.0651351 “1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)” 811774 1.0617336 CGI-49 protein 359887 1.052326 translocase of inner mitochondrial membrane 17 (yeast) homolog A 1709791 1.0378948 BAI1-associated protein 1 244801 1.0162794 Rho guanine exchange factor (GEF) 11 1917941 0.9960315 purine-rich element binding protein B 1858892 0.9897362 hypothetical protein MGC4825 288999 0.9896012 small protein effector 1 of Cdc42 503215 0.9757636 pilin-like transcription factor 1911343 0.967716 “RAB26, member RAS oncogene family” 2029173 0.9672743 “ESTs, Weakly similar to N-WASP [H. sapiens]” 470061 0.9665514 seven in absentia (Drosophila) homolog 2 2016908 0.9615102 “ESTs, Weakly similar to CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR [H. sapiens]” 1469425 0.9610542 SRY (sex determining region Y)-box 22 814054 0.958989 KIAA0040 gene product 814528 0.9569471 “Homo sapiens cDNA: FLJ22139 fis, clone HEP20959” 68636 0.9562688 hypothetical protein MGC2477 290841 0.9562201 “H2B histone family, member A” 236034 0.9534619 “uncoupling protein 2 (mitochondrial, proton carrier)” 782428 0.9524489 KIAA0250 gene product 131094 0.9518372 “Homo sapiens cDNA: FLJ21587 fis, clone COL06946” 488202 0.9501137 “ESTs, Weakly similar to YZ28_HUMAN HYPOTHETICAL PROTEIN ZAP128 [H. sapiens]” 1435862 0.9500093 “antigen identified by monoclonal antibodies 12E7, F21 and O13” 823598 0.9452282 “proteasome (prosome, macropain) 26S subunit, non- ATPase, 12” 1492426 0.9397097 chromosome 19 open reading frame 3 795185 0.9295627 xenotropic and polytropic retrovirus receptor 810558 0.9227709 “proteasome (prosome, macropain) 26S subunit, ATPase, 4” 469686 0.9203022 “Ric (Drosophila)-like, expressed in many tissues” 280375 0.9155003 PRO2000 protein 729975 0.9149894 meningioma expressed antigen 5 (hyaluronidase) 810124 0.9124035 “platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29 kD)” 813281 0.9107661 WW domain-containing protein 1 39884 0.9091807 IMP (inosine monophosphate) dehydrogenase 1 76605 0.9028609 nesca protein 1636092 0.8997881 hypothetical protein FLJ20657 741474 0.8925439 glucose phosphate isomerase 1605426 0.8909868 hypothetical protein FLJ13352 788654 0.8886269 868128 0.8873517 JM4 protein 308466 0.8803492 GTP-binding protein Sara 44292 0.8732235 Homo sapiens mRNA; cDNA DKFZp434C107 (from clone DKFZp434C107) 826256 0.8700831 transmembrane 7 superfamily member 1 (upregulated in kidney) 685516 0.8694652 putative G protein-coupled receptor 810711 0.869424 stearoyl-CoA desaturase (delta-9-desaturase) 753299 0.8679015 hypothetical protein FLJ10504 731044 0.8657953 glutaredoxin 2 824052 0.8650616 chromosome 6 open reading frame 1 843195 0.86501 phosphoserine phosphatase 292770 0.8570995 “Homo sapiens, clone IMAGE: 3627860, mRNA, partial cds” 859761 0.8563964 poliovirus receptor-related 2 (herpesvirus entry mediator B) 347373 0.8555396 “transcription elongation factor B (SIII), polypeptide 1 (15 kD, elongin C)” 1640821 0.8544081 “ESTs, Weakly similar to I78885 serine/threonine-specific protein kinase [H. sapiens]” 704414 0.8520508 small nuclear ribonucleoprotein polypeptides B and B1 810725 0.8510425 “ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21 kD” 782608 0.8507815 mitochondrial ribosomal protein L9 2019223 0.849044 mitochondrial ribosomal protein L17 2110511 0.8471736 artemin 1474955 0.8460414 “TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68 kD (RNA-binding protein 56)” 810612 0.842284 S100 calcium-binding protein A11 (calgizzarin) 744417 0.8409538 carnitine acetyltransferase 969877 0.8382113 “synaptosomal-associated protein, 25 kD” 272529 0.8371698 phosphomannomutase 2 768570 0.8371438 hypothetical protein FLJ11280 824879 0.8366695 hypothetical protein MGC11275 2014034 0.8354357 “methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase” 2054635 0.831532 “proteasome (prosome, macropain) subunit, alpha type, 7” 2052113 0.8307595 hypothetical protein FLJ10903 742595 0.8291965 cyclin-dependent kinase 5 2016648 0.8263671 Homo sapiens mRNA; cDNA DKFZp434N1728 (from clone DKFZp434N1728) 1573251 0.823025 peroxisomal long-chain acyl-coA thioesterase 1869201 0.8202299 hypothetical protein MGC2745 37708 0.8194577 hypothetical protein MGC3101 241348 0.8182422 prenylcysteine lyase 810063 0.8168926 “growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)” 731308 0.8166873 citrate synthase 209066 0.8120797 590774 0.8100386 mitogen-activated protein kinase 13 1435003 0.8098225 tumor suppressing subtransferable candidate 1 502774 0.8091404 hypothetical protein FLJ20623 488505 0.808712 accessory proteins BAP31/BAP29 109863 0.8066906 epithelial membrane protein 2 813419 0.8043966 “hydroxyacyl-Coenzyme A dehydrogenase, type II” 1845169 0.8033348 “RAB35, member RAS oncogene family” 742707 0.7955239 “ESTs, Weakly similar to MUC2_HUMAN MUCIN 2 PRECURSOR [H. sapiens]” 594500 0.7935958 EST 1456701 0.7934389 B-cell CLL/lymphoma 9 271472 0.7901735 C3HC4-like zinc finger protein 1473922 0.7892502 “actin related protein 2/3 complex, subunit 3 (21 kD)” 51773 0.7858986 hypothetical protein MGC3077 898032 0.7852733 KIAA0097 gene product 340558 0.7791736 “actin related protein 2/3 complex, subunit 5 (16 kD)” 773922 0.7767604 KIAA0005 gene product 768064 0.7743382 “cytochrome P450, subfamily I (aromatic compound- inducible), polypeptide 1” 625923 0.7725056 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 150003 0.77183 hypothetical protein FLJ13187 741977 0.7715372 “B-factor, properdin” 365738 0.7709456 ESTs 814350 0.7701748 insulin-degrading enzyme 2108077 0.7700354 CGI-112 protein 209066 0.7693907 serine/threonine kinase 15 564492 0.7672548 mitochondrial carrier homolog 2 366353 0.7664569 DKFZP564C186 protein 813751 0.7659116 “sialyltransferase 4C (beta-galactosidase alpha-2,3- sialytransferase)” 781097 0.7633668 reticulon 3 233349 0.762952 hypothetical protein FLJ10761 825327 0.7622414 “Homo sapiens cDNA FLJ14105 fis, clone MAMMA1001202” 248649 0.761865 hypothetical protein FLJ13910 589232 0.7583348 hypothetical protein FLJ11506 564847 0.757516 ESTs 754628 0.7573763 ESTs 1500162 0.7571399 ESTs 1738208 0.7565056 “a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4” 842994 0.7563101 cathepsin Z 42408 0.7559848 hypothetical protein MGC4604 470124 0.7539249 RAD1 (S. pombe) homolog 809357 0.7535411 Bernardinelli-Seip congenital lipodystrophy 2 (seipin) 624667 0.7524325 CGI-92 protein 49351 0.75115 SEX gene 46248 0.7510436 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 686552 0.7506994 golgi phosphoprotein 1 1631735 0.7505843 “Homo sapiens, clone IMAGE: 3604336, mRNA, partial cds” 1536006 0.7499887 ESTs 83363 0.748646 protein-L-isoaspartate (D-aspartate) O-methyltransferase 713782 0.7484589 a disintegrin and metalloproteinase domain 15 (metargidin) 727078 0.7472345 “Homo sapiens cDNA: FLJ23602 fis, clone LNG15735” 503889 0.7454098 hypothetical protein FLJ10656 284261 0.7445419 uncharacterized hematopoietic stem/progenitor cells protein MDS030 1473289 0.7441483 protective protein for beta-galactosidase (galactosialidosis) 49273 0.742123 “solute carrier family 27 (fatty acid transporter), member 4” 785701 0.7413837 “RAB31, member RAS oncogene family” 41569 0.7412357 hypothetical protein FLJ12650 810402 0.7407907 hypothetical protein 1456348 0.7397574 N-acetylneuraminic acid phosphate synthase; sialic acid synthase 256619 0.7395032 hydroxysteroid (17-beta) dehydrogenase 7 743589 0.7372744 “ESTs, Weakly similar to T2D3_HUMAN TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT [H. sapiens]” 1409509 0.7370811 “troponin T1, skeletal, slow” 122241 0.7352191 “proteasome (prosome, macropain) subunit, beta type, 2” 470099 0.7343404 HT002 protein; hypertension-related calcium-regulated gene 725454 0.7335223 CDC28 protein kinase 2 796694 0.7317383 baculoviral IAP repeat-containing 5 (survivin) 186768 0.7298378 “Homo sapiens, clone IMAGE: 3604869, mRNA” 813629 0.7288266 YME1 (S. cerevisiae)-like 1 842980 0.7284256 developmentally regulated GTP-binding protein 1 769921 0.726646 ubiquitin carrier protein E2-C 2322367 0.7249854 reticulon 4 951233 0.7240615 “proteasome (prosome, macropain) subunit, beta type, 3” 842825 0.7235007 G1 to S phase transition 1 782608 0.7230962 2043167 0.7224903 BCL2-associated athanogene 3 827171 0.7211896 ESTs 120271 0.7208543 hypothetical protein MGC4692 1518890 0.7206844 “metallothionein-like 5, testis-specific (tesmin)” 60565 0.720547 lethal giant larvae (Drosophila) homolog 2 2050827 0.7156518 “proteasome (prosome, macropain) 26S subunit, ATPase, 5” 1635681 0.7152705 “NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8 kD, B8)” 731023 0.7151176 WD repeat domain 5 1518402 0.7150061 KIAA1361 protein 752631 0.7139862 “fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism)” 785616 0.7131593 “signal sequence receptor, alpha (translocon-associated protein alpha)” 686172 0.7131363 KIAA0008 gene product 40173 0.7124913 KIAA0807 protein 123441 0.7124698 ribosomal protein L7a 123614 0.7117834 hypothetical protein MGC4675 811024 0.7117211 bone marrow stromal cell antigen 2 2302099 0.7117055 sialidase 3 (membrane sialidase) 756442 0.7115925 P450 (cytochrome) oxidoreductase 811585 0.7087617 huntingtin (Huntington disease) 279970 0.7040135 adenosine A2a receptor 1517171 0.7036866 “interleukin 2 receptor, alpha” 838366 0.702617 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase (hydroxymethylglutaricaciduria) 809944 0.7021108 KIAA0310 gene product 1393018 0.701717 “general transcription factor IIIC, polypeptide 1 (alpha subunit, 220 kD)” 725978 0.7010756 “ESTs, Moderately similar to ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens]” 325606 0.7008219 hypothetical protein MGC14353 795256 0.6974866 NPD007 protein 365358 0.696963 pM5 protein 67765 0.6967324 carboxypeptidase M 358267 0.6962436 “EST, Moderately similar to AF119917 63 PRO2831 [H. sapiens]” 149355 0.6943923 translocating chain-associating membrane protein 212542 0.6938079 “Homo sapiens cDNA FLJ12900 fis, clone NT2RP2004321” 79520 0.6919579 “RAB2, member RAS oncogene family” 739126 0.6881663 tissue specific transplantation antigen P35B 202514 0.6872212 DNA (cytosine-5-)-methyltransferase 3 alpha 1884404 0.6864546 KIAA0285 gene product 814378 0.6857148 “serine protease inhibitor, Kunitz type, 2” 2018337 0.6828744 “glucosidase, beta; acid (includes glucosylceramidase)” 701751 0.6824676 cut (Drosophila)-like 1 (CCAAT displacement protein) 2018084 0.6822251 Ste-20 related kinase 781019 0.6819736 paraoxonase 2 2244196 0.6807351 B-cell receptor-associated protein BAP29 124447 0.679866 KIAA1184 protein 789012 0.6794432 fibulin 2 490778 0.6788304 low molecular mass ubiquinone-binding protein (9.5 kD) 2011515 0.6774452 DKFZP586B0923 protein 80764 0.6765616 hypothetical protein 841679 0.6762195 calcium and integrin binding protein (DNA-dependent protein kinase interacting protein) 108425 0.6761526 878406 0.6750777 metaxin 1 487733 0.6745496 625693 0.6744622 hypothetical protein MGC10911 1325816 0.6742078 polymerase (RNA) II (DNA directed) polypeptide L (7.6 kD) 278531 0.6737637 cytochrome c oxidase subunit VIc 744374 0.6732551 putative ankyrin-repeat containing protein 203003 0.6724027 “non-metastatic cells 4, protein expressed in” 564981 0.6712134 ESTs 812994 0.671102 “retinoid X receptor, alpha” 172517 0.6701228 hippocalcin-like 1 205049 0.6682666 protein kinase H11; small stress protein-like protein HSP22 1734309 0.6672454 sperm associated antigen 4 1631699 0.6665952 valosin-containing protein 2028949 0.6662774 hypothetical protein PRO1855 530197 0.6659784 “ESTs, Moderately similar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens]” 199645 0.6654138 nicastrin 704254 0.6653635 a disintegrin and metalloproteinase domain 8 1592715 0.6637095 “Homer, neuronal immediate early gene, 3” 302031 0.6626629 Ste20-related serine threonine kinase 239568 0.661735 annexin A9 770785 0.6613519 “1,2-alpha-mannosidase IC” 785795 0.660789 hypothetical protein FLJ12910 810734 0.6603412 “polymerase (DNA-directed), delta 4” 1696757 0.6591801 hypothetical protein KIAA1165 811761 0.6587469 Nijmegen breakage syndrome 1 (nibrin) 150314 0.6584621 lysophospholipase I 489351 0.65846 hypothetical protein DKFZp566J2046 593431 0.6578268 “ESTs, Moderately similar to CEGT_HUMAN CERAMIDE GLUCOSYLTRANSFERASE [H. sapiens]” 37554 0.6574292 hypothetical protein FLJ22353 126851 0.6559601 hypothetical protein FLJ11160 265103 0.6548137 Homo sapiens mRNA; cDNA DKFZp547M123 (from clone DKFZp547M123) 51083 0.6544472 “catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)” 431505 0.6534315 “ESTs, Highly A31026 probable membrane receptor protein [H. sapiens]” 1420370 0.6531171 biliverdin reductase B (flavin reductase (NADPH)) 1476053 0.6522237 RAD51 (S. cerevisiae) homolog (E coli RecA homolog) 882484 0.6521026 “chaperonin containing TCP1, subunit 7 (eta)” 51532 0.6504769 ADP-ribosylation factor-like 6 interacting protein 280249 0.6503028 Kruppel-like factor 7 (ubiquitous) 138788 0.6497728 prolactin receptor 1492468 0.647846 DEME-6 protein 221295 0.6477514 “inhibitor of DNA binding 2, dominant negative helix-loop- helix protein” 897806 0.6470379 “hypoxia-inducible factor 1, alpha subunit (basic helix-loop- helix transcription factor)” 358936 0.6441198 “ESTs, Weakly similar to T2D3_HUMAN TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT [H. sapiens]” 840865 0.644011 “myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)” 788334 0.6427785 mitochondrial ribosomal protein L23 366067 0.6416356 cerebellar degeneration-related protein (62 kD) 825585 0.6413235 tubulin-specific chaperone e 1460110 0.6397172 “proteasome (prosome, macropain) subunit, beta type, 5” 344091 0.6381862 ESTs 196189 0.6338517 cytochrome b-5 2248488 0.6337488 ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate) 509823 0.6334191 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 144880 0.6332999 hypothetical protein from EUROIMAGE 1759349 755599 0.6330221 interferon induced transmembrane protein 1 (9-27) 207288 0.632639 insulin induced gene 1 1639531 0.6315732 “RAB27A, member RAS oncogene family” 144740 0.630134 similar to phosphatidylcholine transfer protein 2 814306 0.630078 tumor protein D52 301122 0.6299499 extracellular matrix protein 1 124298 0.6294358 microsomal glutathione S-transferase 3 1733262 0.6293971 BLu protein 376875 0.6286902 flavin containing monooxygenase 1 773188 0.6270494 “nuclear receptor subfamily 1, group D, member 2” 756666 0.6269882 “protein phosphatase 1, catalytic subunit, alpha isoform” 810156 0.6266313 deoxythymidylate kinase (thymidylate kinase) 2015517 0.6259564 hypothetical protein FLJ22237 770845 0.6253839 hexokinase 1 813707 0.6252347 regulator of G-protein signalling 16 611443 0.6244565 myoglobin 124331 0.624455 “cleavage and polyadenylation specific factor 5, 25 kD subunit” 855800 0.6235647 prolyl endopeptidase 625234 0.62188 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 753378 0.6218232 hypothetical protein FLJ22649 similar to signal peptidase SPC22/23 2055807 0.6216372 protein kinase domains containing protein similar to phosphoprotein C8FW 840878 0.6216124 seladin-1 1700436 0.6215741 ESTs 261472 0.6215341 putative nuclear protein ORF1-FL49 121251 0.6209436 hypothetical protein MGC5576 140289 0.6205892 hypothetical protein 2018821 0.6205344 ATPase inhibitor precursor 770766 0.6193342 DKFZP564C1940 protein 767798 0.6192232 “ATX1 (antioxidant protein 1, yeast) homolog 1” 845363 0.617901 “non-metastatic cells 1, protein (NM23A) expressed in” 120749 0.6172281 “ESTs, Moderately similar to KIAA1215 protein [H. sapiens]” 358162 0.616765 protein predicted by clone 23627 781342 0.6159353 hypothetical protein MGC11115 767761 0.6142782 DKFZP434B168 protein 191904 0.6141265 “BUB3 (budding uninhibited by benzimidazoles 3, yeast) homolog” 726699 0.6131491 “ESTs, Weakly similar to AAB47496 NG5 [H. sapiens]” 2326057 0.61263 MLN51 protein 784140 0.6102245 WD repeat domain 15 770355 0.6099761 “lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)” 81336 0.6099072 uteroglobin 757328 0.6097389 hypothetical protein FLJ22678 773674 0.6095732 oncogene TC21 289978 0.6090234 ubiquitin-like 4 66535 0.6088919 ornithine decarboxylase antizyme 2 826363 0.6087183 lysophospholipase II 1758590 0.6074571 “fatty-acid-Coenzyme A ligase, long-chain 3” 1553306 0.6066787 “proteasome (prosome, macropain) 26S subunit, non- ATPase, 11” 785766 0.6058332 hypothetical protein 725841 0.6051304 KIAA0662 gene product 2020898 0.6044163 “procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3” 504308 0.6041122 hypothetical protein FLJ10540 510575 0.6040713 hypothetical protein FLJ22087 49630 0.6027878 “calcium channel, voltage-dependent, L type, alpha 1D subunit” 142586 0.602037 MCT-1 protein 725284 0.6014099 “phosphorylase kinase, gamma 2 (testis)” 429799 0.6012713 hypothetical protein FLJ21939 similar to 5-azacytidine induced gene 2 1474424 0.6006702 “Homo sapiens cDNA FLJ12758 fis, clone NT2RP2001328” 784105 0.6003082 ESTs 2018527 0.599584 dolichyl-phosphate mannosyltransferase polypeptide 3 855563 0.5987092 v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 823574 0.5978052 endosulfine alpha 323693 0.5975785 “adaptor-related protein complex 1, sigma 1 subunit” 824962 0.595868 “karyopherin alpha 2 (RAG cohort 1, importin alpha 1)” 773426 0.5941568 KIAA0391 gene product 772925 0.5940171 HSPCO34 protein 1656062 0.593408 coagulation factor XII (Hageman factor) 825740 0.5931142 DKFZp434J1813 protein 376516 0.5906248 cell division cycle 4-like 292213 0.5883092 “guanine nucleotide binding protein (G protein), beta polypeptide 2” 1898619 0.5880791 hypothetical protein MGC15737 414992 0.587733 K562 cell-derived leucine-zipper-like protein 1 1573946 0.5875624 programmed cell death 9 739109 0.5874334 “adaptor-related protein complex 2, sigma 1 subunit” 430235 0.585372 “H2B histone family, member Q” 2572170 0.5852444 “ESTs, Weakly similar to T26581 hypothetical protein Y32B12A.3 - Caenorhabditis elegans [C. elegans]” 487733-2 0.5844776 “NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2 (8 kD, AGGG)” 1698036 0.5843382 ubiquitin-conjugating enzyme E2 variant 1 127646 0.5838788 346696 0.5838269 TEA domain family member 4 74738 0.5835427 “Homo sapiens, clone IMAGE: 3535294, mRNA, partial cds” 124781 0.5832065 squalene epoxidase 1883028 0.5828007 Homo sapiens mRNA; cDNA DKFZp434J1912 (from clone DKFZp434J1912) 183200 0.5801312 fumarylacetoacetate hydrolase (fumarylacetoacetase) 51741 0.5795151 GTP-binding protein 590759 0.5791873 sterol-C4-methyl oxidase-like 755301 0.5790795 “protein kinase C, delta” 843054 0.5776102 KIAA1533 protein 595213 0.5775511 hypothetical protein 752643 0.5774681 group XII secreted phospholipase A2 141852 0.5762886 “purinergic receptor P2Y, G-protein coupled, 2” 813631 0.5754418 seven transmembrane protein TM7SF3 1601947 0.5744444 cytochrome c oxidase subunit VIIa polypeptide 2 (liver) 51657 0.5736969 hypothetical protein ET 814209 0.5736866 ESTs 72050 0.5722845 “chloride channel, nucleotide-sensitive, 1A” 1635665 0.5714089 “Homo sapiens, RIKEN cDNA 2010100O12 gene, clone MGC: 14813 IMAGE: 4133274, mRNA, complete cds” 66406 0.5706229 hypothetical protein DKFZp762E1312 530310 0.5686743 KIAA0143 protein 41356 0.5683316 “protein phosphatase 2, regulatory subunit B (B56), alpha isoform” 1844765 0.5670398 Homo sapiens mRNA; cDNA DKFZp564O1763 (from clone DKFZp564O1763) 489823 0.5666593 “COX17 (yeast) homolog, cytochrome c oxidase assembly protein” 1517749 0.5665848 ESTs 813410 0.5664086 polymerase (RNA) II (DNA directed) polypeptide K (7.0 kD) 1416782 0.5657017 “creatine kinase, brain” 1422338 0.5652946 ribonucleotide reductase M2 polypeptide 250313 0.5649247 ESTs 235986 0.5649127 “wingless-type MMTV integration site family, member 11” 66317 0.5648355 “H1 histone family, member 2” 279720 0.5645072 “ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens]” 884498 0.5640535 uncharacterized hypothalamus protein HT012 503851 0.564048 nuclear receptor co-repressor/HDAC3 complex subunit 823930 0.5633774 “actin related protein 2/3 complex, subunit 1A (41 kD)” 120271 0.5626611 hypothetical protein MGC4692 782513 0.5625811 “interferon, alpha-inducible protein (clone IFI-6-16)” 246800 0.5625675 hypothetical protein FLJ10803 2309073 0.5617024 frizzled (Drosophila) homolog 5 784150 0.5598483 “RAB31, member RAS oncogene family” 139835 0.5590106 UDP-glucose dehydrogenase 1641894 0.5587185 EST 796757 0.5585876 “adaptor-related protein complex 3, sigma 1 subunit” 813616 0.5574238 FK506-binding protein like 2549634 0.5572052 activator of S phase kinase 741769 0.5565863 “polymerase (DNA directed), beta” 488642 0.5560728 “ESTs, Weakly similar to I38022 hypothetical protein [H. sapiens]” 795498 0.5557245 putative transmembrane protein 1492780 0.5555908 “Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409” 241043 0.5545302 “Human clone 137308 mRNA, partial cds” 295986 0.5544422 emopamil-binding protein (sterol isomerase) 839682 0.5542571 ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13) 1581941 0.5537015 hypothetical protein FLJ14540 809466 0.5532437 DNA segment on chromosome 19 (unique) 1177 expressed sequence 1947381 0.5524634 hypothetical protein FLJ22329 825470 0.5523318 topoisomerase (DNA) II alpha (170 kD) 1848977 0.5519913 glycerol kinase 700792 0.5493223 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 825386 0.5487104 “ATP synthase, H+ transporting, mitochondrial F1F0, subunit d” 826194 0.5486839 synaptotagmin-like 2 299815 0.5485843 hypothetical protein DC42 1753497 0.5485231 ovo (Drosophila) homolog-like 1 744944 0.5482368 myosin VI 1499828 0.5479012 “fucosyltransferase 1 (galactoside 2-alpha-L- fucosyltransferase, Bombay phenotype included)” 415102 0.5465851 cell division cycle 25C 813387 0.5460577 diaphorase (NADH/NADPH) (cytochrome b-5 reductase) 786265 0.5443881 KIAA0750 gene product 1591264 0.5440944 transaldolase 1 756595 0.5433619 “S100 calcium-binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11))” 855749 0.5432466 triosephosphate isomerase 1 470092 0.5429717 like-glycosyltransferase 244764 0.5424555 B7 homolog 3 1637282 0.542121 hexokinase 2 417801 0.5414761 mitochondrial ribosomal protein L27 826077 0.5405591 pyruvate dehydrogenase (lipoamide) beta 757489 0.5386267 “tubulin, alpha 2” 327635 0.5368033 adenylate kinase 1 343731 0.5365018 786067 0.5361882 cell division cycle 25B 2017415 0.5353408 centromere protein A (17 kD) 292996 0.5341429 “tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide” 815781 0.5340254 heat shock 105 kD 346942 0.5326646 “phosphatidylinositol glycan, class Q” 823694 0.5321203 “Homo sapiens chromosome 19, BAC CIT-HSPC_204F22 (BC228680), complete sequence; contains bacterial insertion element” 139354 0.5318709 hypothetical protein 221499 0.5317861 KIAA0508 protein 263727 0.5313082 “DNA segment, single copy probe LNS-CAI/LNS-CAII (deleted in polyposis” 489594 0.5308806 hypothetical protein FLJ11565 824524 0.5296138 UDP-galactose transporter related 951216 0.5291832 “NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22 kD, PDSW)” 841260 0.5285587 hypothetical protein 283739 0.5276555 “Homo sapiens cDNA FLJ14028 fis, clone HEMBA1003838” 49117 0.5274035 KIAA0215 gene product 1762111 0.5272967 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 358609 0.5266332 NADH dehydrogenase (ubiquinone) flavoprotein 3 (10 kD) 884425 0.5265114 “chaperonin containing TCP1, subunit 5 (epsilon)” 795401 0.5264278 diacylglycerol O-acyltransferase (mouse) homolog 811907 0.5246416 hypothetical protein FLJ22056 1631747 0.5245873 male-enhanced antigen 365060 0.5244569 “RAB11A, member RAS oncogene family” 743220 0.5242028 hypothetical protein FLJ12517 705064 0.5238148 “transforming, acidic coiled-coil containing protein 3” 768452 0.5237494 “Homo sapiens EST from clone 491476, full insert” 743977 0.5237158 Homo sapiens mRNA for TL132 1568825 0.5205165 Arg/Abl-interacting protein ArgBP2 772898 0.520392 ribosomal protein S15a 366834 0.5191005 envoplakin 1616253 0.5190257 breast carcinoma amplified sequence 1 322617 0.5188645 v-ral simian leukemia viral oncogene homolog B (ras related; GTP binding protein) 825296 0.5178447 low density lipoprotein receptor defect C complementing 491524 0.5175752 mitochondrial ribosomal protein L13 143426 0.5173212 “ras homolog gene family, member B” 73009 0.516678 “ESTs, Weakly similar to A43932 mucin 2 precursor, intestinal [H. sapiens]” 293569 0.5162069 chromosome 1 open reading frame 21 296702 0.5162041 “deiodinase, iodothyronine, type I” 773286 0.5158979 “solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1” 726658 0.5157542 “non-metastatic cells 3, protein expressed in” 753897 0.5153412 autocrine motility factor receptor 293727 0.5153298 hypothetical protein MGC861 810947 0.5151346 “LIS1-interacting protein NUDE1, rat homolog” 491465 0.5150527 hypothetical protein FLJ10035 814899 0.5142481 BCL2/adenovirus E1B 19 kD-interacting protein 3-like 266500 0.5135558 ESTs 1159963 0.5133656 interferon regulatory factor 7 785707 0.5133005 protein regulator of cytokinesis 1 346134 0.5132068 calcium-regulated heat-stable protein (24 kD) 486110 0.5127183 profilin 2 2017403 0.5117711 regulator of G-protein signalling 3 491527 0.5116183 “Homo sapiens, Similar to CG7083 gene product, clone MGC: 10534 IMAGE: 3957147, mRNA, complete cds” 769600 0.5106262 uracil-DNA glycosylase 2 1558233 0.5101529 ESTs 649084 0.5099122 carbonic anhydrase XI 825822 0.5097808 hypothetical protein 1461477 0.509331 Homo sapiens mRNA; cDNA DKFZp586I0324 (from clone DKFZp586I0324) 327506 0.5092192 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 327506 769942 0.509086 kinesin-like 4 505289 0.5080495 “angiotensin II, type I receptor-associated protein” 726439 0.5080059 CGI-143 protein 79726 0.5078677 “ESTs, Highly similar to T46395 hypothetical protein DKFZp434I1120.1 [H. sapiens]” 810762 0.5072899 SNARE protein 785793 0.5072717 “capping protein (actin filament) muscle Z-line, alpha 1” 81599 0.5067033 ubiquitin specific protease 14 (tRNA-guanine transglycosylase) 294397 0.5066683 DKFZP586A0522 protein 1947647 0.5064941 CGI-147 protein 795805 0.5064099 KIAA0332 protein 810959 0.505619 Rho GDP dissociation inhibitor (GDI) alpha 2322223 0.5047814 small nuclear ribonucleoprotein polypeptide A 472103 0.503987 “soc-2 (suppressor of clear, C. elegans) homolog” 810609 0.5036493 hypothetical protein PP1226 897813 0.5034689 polyadenylate binding protein-interacting protein 1 1500542 0.5032679 regulator of G-protein signalling 11 839746 0.5031787 “Homo sapiens, Similar to RIKEN cDNA 5830420C20 gene, clone IMAGE: 3633379, mRNA, partial cds” 343607 0.5029133 AD-015 protein 649977 0.5002695 Homo sapiens clone CDABP0014 mRNA sequence 823940 0.4997308 “transducer of ERBB2, 1” 2250839 0.4994848 androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease) 731080 0.4979864 hypothetical protein FLJ12661 753400 0.496254 CGI-204 protein 869375 0.4958886 “isocitrate dehydrogenase 2 (NADP+), mitochondrial” 154610 0.4948571 dynactin 4 130835 0.4946783 “Homo sapiens, Similar to clone FLB3816, clone IMAGE: 3454380, mRNA” 859228 0.4942316 “isocitrate dehydrogenase 1 (NADP+), soluble” 41698 0.4938629 progesterone binding protein 30170 0.4936252 “caspase 3, apoptosis-related cysteine protease” 266218 0.4934791 hypothetical protein FLJ11350 509588 0.49319 “TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20 kD” 1916575 0.4923447 BCL2-interacting killer (apoptosis-inducing) 744994 0.4916322 hypothetical protein FLJ12242 487444 0.4887966 “cyclic AMP phosphoprotein, 19 kD” 503866 0.4884193 sperm autoantigenic protein 17 814353 0.4883684 phorbol-12-myristate-13-acetate-induced protein 1 815501 0.4879053 hypothetical protein MGC2721 746163 0.4863317 “ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens]” 347726 0.4837701 homeo box D8 897770 0.4836347 1854539 0.4824023 GAP-associated tyrosine phosphoprotein p62 (Sam68) 41123 0.481642 “Homo sapiens, Similar to RIKEN cDNA 2210021G21 gene, clone MGC: 14859 IMAGE: 3621871, mRNA, complete cds” 856447 0.4816395 “interferon, gamma-inducible protein 30” 1568561 0.4808662 BCL2-like 1 744047 0.4802334 polo (Drosophia)-like kinase 290101 0.4800598 ESTs 455275 0.4788778 hypothetical protein FLJ23469 2069602 0.4786416 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 592801 0.4785497 “serine palmitoyltransferase, long chain base subunit 2” 741891 0.4775456 “RAB2, member RAS oncogene family-like” 1434948 0.4771454 HIV TAT specific factor 1 430614 0.476288 “2,3-bisphosphoglycerate mutase” 454896 0.4760701 “DnaJ (Hsp40) homolog, subfamily A, member 2” 268946 0.4751692 WD40 protein Ciao1 1572710 0.4750848 hypothetical protein FLJ21213 626318 0.4746692 ubinuclein 1 377384 0.4746085 “nuclear receptor subfamily 2, group F, member 2” 1632252 0.474559 “complement component 1, q subcomponent, alpha polypeptide” 489444 0.4741367 hypothetical protein FLJ20211 345787 0.4734963 “highly expressed in cancer, rich in leucine heptad repeats” 767487 0.4729158 “ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1” empty-31 0.4726918 blank 135640 0.4708685 syntaxin 3A 754653 0.4707927 “cadherin, EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog” 1557637 0.4705061 ESTs 788641 0.4703576 “adaptor-related protein complex 1, sigma 2 subunit” 810567 0.4702908 “Homo sapiens, clone MGC: 3182 IMAGE: 3356293, mRNA, complete cds” 366039 0.4701924 KIAA0892 protein 781047 0.4699376 budding uninhibited by benzimidazoles 1 (yeast homolog) 782688 0.4694868 “dynein, axonemal, light intermediate polypeptide” 210862 0.4692392 “acyl-Coenzyme A oxidase 1, palmitoyl” 510794 0.4691467 c-myc binding protein 121436 0.4691298 “Homo sapiens, clone MGC: 4677 IMAGE: 3532809, mRNA, complete cds” 325515 0.4689353 hypothetical protein FLJ10980 965223 0.4687291 “thymidine kinase 1, soluble” 1469148 0.467634 FGFR1 oncogene partner 149539 0.4671676 KIAA1700 2306987 0.4670155 secreted and transmembrane 1 122147 0.4652151 2063982 0.4651856 “potassium channel, subfamily K, member 6 (TWIK-2)” 769890 0.4647115 nucleoside phosphorylase 1642496 0.4645092 hypothetical protein MGC11266 428582 0.4642013 hypothetical protein FLJ20296 66599 0.4639123 N-acetyltransferase 1 (arylamine N-acetyltransferase) 1565455 0.4634802 “nuclear receptor subfamily 2, group C, member 2” 810939 0.4634658 hypothetial protein FLJ22169 359723 0.4630712 mitochondrial elongation factor G 1027283 0.4628012 ESTs 1636844 0.4627748 ring finger protein 14 469151 0.4622121 “eukaryotic translation initiation factor 2, subunit 2 (beta, 38 kD)” 813675 0.4614894 “Human D9 splice variant B mRNA, complete cds” 489657 0.4609514 tryptophan rich basic protein 469383 0.4607375 chromosome 8 open reading frame 1 40042 0.4604322 hypothetical protein FLJ10747 726637 0.45959 t-complex-associated-testis-expressed 1-like 811142 0.4595393 “phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)” 179212 0.4594831 “ESTs, Moderately similar to T12539 hypothetical protein DKFZp434J154.1 [H. sapiens]” 292936 0.4593712 hypothetical protein FLJ10468 2046679 0.4579596 ESTs 810497 0.4572069 “ESTs, Weakly similar to A35363 synapsin I splice form a [H. sapiens]” 1585492 0.4571478 ESTs 782689 0.4570254 “solute carrier family 6 (neurotransmitter transporter, creatine), member 8” 774446 0.4567242 adrenomedullin 366156 0.4563893 “Homo sapiens cDNA FLJ14028 fis, clone HEMBA1003838” 725649 0.4559473 “nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4” 76362 0.4553121 “spectrin, alpha, non-erythrocytic 1 (alpha-fodrin)” 754046 0.4550413 DNA segment on chromosome X (unique) 9879 expressed sequence 345538 0.4550133 cathepsin L 782439 0.454474 “ATP synthase, H+ transporting, mitochondrial F0 complex, subunit e” 1537001 0.4539586 ESTs 345423 0.4538841 DKFZP564M112 protein 1702742 0.453453 “solute carrier family 7 (cationic amino acid transporter, y+ system), member 5” 825659 0.4515758 N-myc downstream regulated 1652310 0.4512689 “Homo sapiens, clone MGC: 19613 IMAGE: 3833049, mRNA, complete cds” 1523225 0.4511104 oncostatin M receptor 40773 0.4510289 “guanine nucleotide binding protein (G protein), alpha z polypeptide” 35626 0.4509825 “Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955” 358217 0.4507923 glypican 4 214996 0.45033 ESTs 177827 0.4500254 synaptotagmin VII 1075635 0.4495618 MLSN1- and TRP-related 810039 0.4491986 defender against cell death 1 772220 0.4475721 for protein disulfide isomerase-related 70606 0.4475592 ESTs 1692195 0.4471181 smg GDS-ASSOCIATED PROTEIN 841621 0.4466003 “ESTs, Weakly similar to JE0350 Anterior gradient-2 [H. sapiens]” 855707 0.4456433 ESTs 1455394 0.4455695 cytochrome c 85804 0.44449 hypothetical protein FLJ21918 809512 0.4442565 hypothetical protein FLJ10767 753457 0.4435792 NADH dehydrogenase (ubiquinone) Fe—S protein 1 (75 kD) (NADH-coenzyme Q reductase) 767289 0.4432685 hypothetical protein FLJ10055 565235 0.4428854 spermine synthase 611467 0.4428543 NADH dehydrogenase (ubiquinone) Fe—S protein 6 (13 kD) (NADH-coenzyme Q reductase) 812105 0.4424976 ALL1-fused gene from chromosome 1q 1558642 0.4424721 hypothetical protein MGC2771 814989 0.4419384 “protein phosphatase 1G (formerly 2C), magnesium- dependent, gamma isoform” 1899312 0.4418248 ESTs 1486533 0.441804 keratin 16 (focal non-epidermolytic palmoplantar keratoderma) 1565079 0.4415966 B-cell linker 783681 0.4412503 upstream regulatory element binding protein 1 1422723 0.4411931 interferon-induced protein 35 785368 0.4411742 PDZ-binding kinase; T-cell originated protein kinase 1517595 0.4409591 KIAA0175 gene product 713862 0.4400704 ubiquitin-protein isopeptide ligase (E3) 83358 0.4397161 ESTs 81203 0.4391758 paraoxonase 3 74070 0.4390933 endosulfine alpha 2306221 0.4385881 “wingless-type MMTV integration site family, member 10B” 140635 0.4384907 ESTs 150118 0.4383146 hypothetical protein DKFZp434F054 214068 0.4383007 GATA-binding protein 3 1434905 0.4382073 homeo box B7 450301 0.4380657 mutL (E. coli) homolog 3 2027952 0.437854 hypothetical protein FLJ20297 745394 0.4374406 “Homo sapiens cDNA: FLJ23249 fis, clone COL04196” 824108 0.4369933 SCAN domain-containing 1 795543 0.4364791 thioredoxin peroxidase (antioxidant enzyme) 1592837 0.4355927 interferon induced transmembrane protein 2 (1-8D) 77533 0.435582 “inositol polyphosphate-5-phosphatase, 40 kD” 1583198 0.4350835 “ESTs, Weakly similar to S65824 reverse transcriptase homolog [H. sapiens]” 84295 0.4349213 interleukin 1 receptor antagonist 770992 0.4346858 837864 0.4345283 progestin induced protein 1909574 0.4342055 mitochondrial ribosomal protein S11 128695 0.4340119 “ESTs, Weakly similar to I38344 titin, cardiac muscle [H. sapiens]” 742581 0.433453 “Homo sapiens cDNA FLJ10366 fis, clone NT2RM2001420” 52103 0.432756 hypothetical protein FLJ23045 770675 0.4319407 “Homo sapiens cDNA: FLJ21323 fis, clone COL02374” 756373 0.4310628 Rho guanine exchange factor (GEF) 16 43977 0.4309655 KIAA0182 protein 2322079 0.4309341 25440 0.4304195 “staufen (Drosophila, RNA-binding protein) homolog 2” 207794 0.4297389 “nuclear factor (erythroid-derived 2), 45 kD” 746190 0.4291743 hypothetical protein DKFZp761B1514 74566 0.4279059 “exportin 1 (CRM1, yeast, homolog)” 76196 0.4278385 hypothetical protein FLJ20062 826173 0.4276784 profilin 1 1587863 0.4270229 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3- oxoacyl-Coenzyme A thiolase) 2017721 0.4268089 “ESTs, Weakly similar to 2109260A B cell growth factor [H. sapiens]” 809464 0.426456 “fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)” 41826 0.4264531 ESTs 1687976 0.4257058 “endoplasmic reticulum chaperone SIL1, homolog of yeast” 416436 0.4252319 mitochondrial ribosomal protein L24 145491 0.4250102 protocadherin 1 (cadherin-like 1) 810316 0.4245985 very long-chain acyl-CoA synthetase; lipidosin 629944 0.4242364 myosin VB 1637302 0.424164 DNAJ domain-containing 754625 0.4236648 “ATPase, Class II, type 9A” 298417 0.4235025 trefoil factor 3 (intestinal) 47853 0.4231314 “aldehyde dehydrogenase 4 family, member A1” 809727 0.4224266 unc-51 (C. elegans)-like kinase 1 774502 0.4222849 “protein tyrosine phosphatase, non-receptor type 12” 785840 0.4219115 “SEC24 (S. cerevisiae) related gene family, member D” 823907 0.4218216 hypothetical protein FLJ10511 1679942 0.4215618 KIAA1053 protein 823909 0.4215098 1600239 0.421459 HSPC037 protein 85195 0.4207753 “growth arrest and DNA-damage-inducible, gamma” 1640282 0.4205899 KIAA1240 protein 782503 0.4205398 fatty acid desaturase 1 266312 0.4201146 “ATPase, Cu++ transporting, beta polypeptide (Wilson disease)” 884511 0.4199518 cytochrome c oxidase subunit VIIb 2051697 0.4197703 “inhibitor of kappa light polypeptide gene enhancer in B- cells, kinase beta” 724888 0.4196322 “cytochrome P450, subfamily IVB, polypeptide 1” 809507 0.4189998 hypothetical protein FLJ20568 151449 0.4189856 “protein tyrosine phosphatase, non-receptor type 21” 743860 0.4189656 “hypothetical protein, clone 2746033” 345833 0.4187433 heterogeneous nuclear ribonucleoprotein A/B 259950 0.4187278 hypothetical protein FLJ14991 283751 0.4179154 cortistatin 810875 0.4176896 “solute carrier family 26, member 6” 26883 0.4176151 “protein kinase (cAMP-dependent, catalytic) inhibitor beta” 38356 0.4173012 “cytochrome P450, subfamily 46 (cholesterol 24- hydroxylase)” 35191 0.4165847 stromal cell-derived factor 2 75859 −2.4150177 N-myc downstream-regulated gene 2 1569187 −1.9090486 heparan sulfate (glucosamine) 3-O-sulfotransferase 4 345670 −1.889471 “ESTs, Moderately similar to I59348 CCAAT binding transcription factor CBF subunit C - rat [R. norvegicus]” 760299 −1.8654555 dickkopf (Xenopus laevis) homolog 3 753071 −1.8417236 “Homo sapiens cDNA: FLJ22528 fis, clone HRC12825” 344720 −1.7951928 glycophorin C (Gerbich blood group) 810002 −1.7256692 “Homo sapiens, clone MGC: 19762 IMAGE: 3636045, mRNA, complete cds” 200814 −1.7140538 “membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10)” 131839 −1.7087069 folate receptor 1 (adult) 300632 −1.6969092 hypothetical protein FLJ21044 similar to Rbig1 811920 −1.6924158 “interleukin 11 receptor, alpha” 486683 −1.6799604 Homo sapiens mRNA; cDNA DKFZp564J0323 (from clone DKFZp564J0323) 1558675 −1.6577507 SRY (sex determining region Y)-box 10 840266 −1.6530726 “Homo sapiens cDNA: FLJ22667 fis, clone HSI08385” 285377 −1.6514168 pellino (Drosophila) homolog 2 1469377 −1.6473741 lipoma HMGIC fusion partner-like 2 45099 −1.6325981 regucalcin (senescence marker protein-30) 1161564 −1.5917197 desmuslin 298122 −1.5678888 frizzled (Drosophila) homolog 7 796542 −1.5553964 ets variant gene 5 (ets-related molecule) 289760 −1.5534789 “ESTs, Highly similar to T00391 hypothetical protein KIAA0612 [H. sapiens]” 22917 −1.5156635 Homo sapiens mRNA; cDNA DKFZp761M0111 (from clone DKFZp761M0111) 838478 −1.5059801 neurocalcin delta 788234 −1.4824055 “inhibitor of DNA binding 4, dominant negative helix-loop- helix protein” 377461 −1.4787671 “caveolin 1, caveolae protein, 22 kD” 67741 −1.4786722 PP2135 protein 839736 −1.4745405 “crystallin, alpha B” 712139 −1.4736508 ADP-ribosylation factor-like 7 160192 −1.4695435 “ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens]” 742685 −1.4440371 disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein) 1556433 −1.4191955 GRO3 oncogene 1554167 −1.4126653 hypothetical protein FLJ14529 877621 −1.3987023 nGAP-like protein 1882697 −1.3873266 peanut (Drosophila)-like 2 72778 −1.3873177 “caspase 7, apoptosis-related cysteine protease” 666879 −1.3624072 annexin A8 69002 −1.3581187 PPAR(gamma) angiopoietin related protein 811848 −1.3549757 hypothetical protein 490023 −1.3516302 hypothetical protein MGC2648 781017 −1.3232108 early growth response 2 (Krox-20 (Drosophila) homolog) 767202 −1.3217103 latent transforming growth factor beta binding protein 2 291478 −1.3155899 runt-related transcription factor 3 757191 −1.2902603 ESTs 130201 −1.2885369 intercellular adhesion molecule 2 1635320 −1.2878152 “amiloride-sensitive cation channel 2, neuronal” 140574 −1.2754214 “small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)” 416676 −1.2751042 pellino (Drosophila) homolog 1 814798 −1.2748689 “aldehyde dehydrogenase 1 family, member A3” 611532 −1.273871 “troponin I, skeletal, fast” 2056139 −1.2697411 LIM domain protein 377275 −1.2665702 ataxia-telangiectasia group D-associated protein 303109 −1.2557454 purinergic receptor (family A group 5) 813265 −1.2549431 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 878836 −1.2507242 “secretory granule, neuroendocrine protein 1 (7B2 protein)” 1473471 −1.2409979 KIAA0194 protein 529843 −1.2405917 “ESTs, Moderately similar to JC5238 galactosylceramide- like protein, GCP [H. sapiens]” 505864 −1.2393277 RalGDS-like gene 781014 −1.2359239 suppression of tumorigenicity 5 470393 −1.2354879 “matrix metalloproteinase 7 (matrilysin, uterine)” 290378 −1.2346086 podocalyxin-like 196435 −1.2282733 ESTs 71087 −1.2181178 “v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein F” 34093 −1.2156885 EST 76182 −1.2102812 hypothetical protein DKFZp761F241 884462 −1.2078038 Down syndrome critical region gene 1 277571 −1.2030738 KIAA1706 protein 841308 −1.200964 “myosin, light polypeptide kinase” 162308 −1.2006293 ESTs 52419 −1.2004086 Friedreich ataxia region gene X123 488404 −1.1981268 Homo sapiens clone TUA8 Cri-du-chat region mRNA 712401 −1.193113 “phosphoinositide-3-kinase, catalytic, delta polypeptide” 289428 −1.1923798 “neurotrophic tyrosine kinase, receptor, type 2” 814443 −1.1905978 hypothetical protein MGC3232 153760 −1.1793765 EphB1 1917449 −1.1785893 “serum amyloid A4, constitutive” 1493218 −1.164886 hypothetical protein FLJ22297 843070 −1.1647509 nucleoporin 88 kD 753038 −1.1629978 kinesin family member C3 811088 −1.1625002 ephrin-B3 2106144 −1.1619925 regulated in glioma 796181 −1.1584587 growth arrest-specific 6 1257131 −1.1566479 ESTs 1473274 −1.1557062 “myosin regulatory light chain 2, smooth muscle isoform” 208718 −1.1498532 annexin A1 811837 −1.1468554 eukaryotic translation elongation factor 1 alpha 1 768571 −1.1461886 SRY (sex determining region Y)-box 8 1474900 −1.1347123 keratin 15 756708 −1.1346161 “potassium intermediate/small conductance calcium- activated channel, subfamily N, member 4” 1555924 −1.1342985 CSR1 protein 811837 −1.1269309 1878409 −1.1144369 catechol-O-methyltransferase 786069 −1.1143906 beta-site APP-cleaving enzyme 815737 −1.1116223 “ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle” 132857 −1.0989746 Homo sapiens mRNA; cDNA DKFZp586N1323 (from clone DKFZp586N1323) 1871116 −1.0975491 Homo sapiens mRNA; cDNA DKFZp434C1714 (from clone DKFZp434C1714); partial cds 133236 −1.0945253 “RNA binding motif protein, X chromosome” 283023 −1.0825166 chemokine (C—X3—C) receptor 1 2016775 −1.0761731 “G protein-coupled receptor, family C, group 5, member B” 897963 −1.0751021 phosphatidic acid phosphatase type 2A 814316 −1.0654718 ribosomal protein L13 47043 −1.0559861 tensin 625399 −1.0523138 hypothetical protein similar to beta-transducin family 416959 −1.051868 nuclear factor I/B 366100 −1.0467604 matrilin 2 753162 −1.0416438 KIAA0603 gene product 491403 −1.0411657 “tumor necrosis factor receptor superfamily, member 1B” 813256 −1.0407652 “ATP-binding cassette, sub-family B (MDR/TAP), member 1” 740620 −1.0395569 tropomyosin 2 (beta) 1577736 −1.035115 epidermal growth factor (beta-urogastrone) 70245 −1.0348655 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 50374 1626996 −1.0328113 c-fos induced growth factor (vascular endothelial growth factor D) 360254 −1.0325653 “cysteine-rich, angiogenic inducer 61” 80344 −1.0323882 interleukin 7 receptor 530958 −1.0316423 smoothened (Drosophila) homolog 34150 −1.0302576 ESTs 809784 −1.030253 “kallikrein 6 (neurosin, zyme)” 990881 −1.0289558 416434 −1.0284229 SCN Circadian Oscillatory Protein (SCOP) 162308 −1.023071 796475 −1.0217348 four and a half LIM domains 3 32489 −1.0196444 hypothetical protein DKFZp566A1524 2504881 −1.0194516 signal transducer and activator of transcription 5A 188335 −1.0161259 “egf-like module containing, mucin-like, hormone receptor- like sequence 2” 593023 −1.0135883 “dystrobrevin, beta” 139660 −1.0134677 ESTs 772913 −1.0122192 calreticulin 270826 −1.0112851 “Homo sapiens cDNA FLJ13329 fis, clone OVARC1001795” 1864302 −1.0099902 E74-like factor 5 (ets domain transcription factor) 1587710 −1.0092611 period (Drosophila) homolog 1 1584540 −1.0077508 Homo sapiens mRNA; cDNA DKFZp586M2022 (from clone DKFZp586M2022) 788136 −1.0073983 “phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)” 40027 −1.0057005 ESTs 1856063 −1.0036618 tweety (Drosophila) homolog 1 209537 −0.9988461 zinc finger protein 221 628955 −0.997687 forkhead box O1A (rhabdomyosarcoma) 2095066 −0.9972552 “alcohol dehydrogenase 1C (class I), gamma polypeptide” 1636166 −0.9969091 KIAA0668 protein 882248 −0.9965858 transgelin 415816 −0.9954308 ESTs 897731 −0.9927981 latrophilin 868396 −0.9916319 “tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide” 343760 −0.9907562 SH3 domain binding glutamic acid-rich protein like 2 1572298 −0.9906095 “CD3Z antigen, zeta polypeptide (TiT3 complex)” 1474337 −0.986117 “phosphorylase, glycogen; brain” 1609665 −0.9851713 BarH-like homeobox 2 2243051 −0.9835274 kallikrein 8 (neuropsin/ovasin) 27544 −0.9834143 prominin (mouse)-like 1 281190 −0.9830533 ESTs 161456 −0.9820939 serum amyloid A1 505243 −0.980381 “inositol 1,4,5-triphosphate receptor, type 2”

Example IV Genes for Discriminating Between Normal and ADH

As shown in Table 3 below, 600 genes were identified as being able to discriminate between normal and ADH. TABLE 3 CloneID Weight Description 1323448 1.3237504 cysteine-rich protein 1 (intestinal) 594500 1.158305 EST 824052 1.034408 chromosome 6 open reading frame 1 149539 0.9878366 KIAA1700 788654 0.9585887 growth factor receptor-bound protein 2 1517749 0.947675 ESTs 1492238 0.9155471 HSPC003 protein 366353 0.9154768 DKFZP564C186 protein 1609836 0.898716 glutamate-ammonia ligase (glutamine synthase) 138189 0.8950816 Wolfram syndrome 1 (wolframin) 344959 0.8945717 gene for serine/threonine protein kinase 1435862 0.8934643 antigen identified by monoclonal antibodies 12E7, F21 and O13 2014373 0.8820247 HNK-1 sulfotransferase 23776 0.879215 quinoid dihydropteridine reductase 293569 0.8708985 chromosome 1 open reading frame 21 130835 0.8659688 Homo sapiens, Similar to clone FLB3816, clone IMAGE: 3454380, mRNA 236034 0.8541082 uncoupling protein 2 (mitochondrial, proton carrier) 488025 0.8525751 Kruppel-associated box protein 178805 0.8524069 Human DNA sequence from clone RP5-850E9 on chromosome 20. Contains part of the gene for a novel C2H2 type zinc finger protein similar to Drosophila Scratch (Scrt), Slug and Xenopus Snail, a novel gene similar to Drosophila CG6762, STSs, GSSs and five CpG 745606 0.8514931 hypothetical protein PP591 1492463 0.8378401 selenoprotein X, 1 530197 0.8206765 ESTs, Moderately similar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 898222 0.8092364 Homo sapiens clone 24418 mRNA sequence 782608 0.8041049 mitochondrial ribosomal protein L9 450301 0.8030667 mutL (E. coli) homolog 3 196189 0.7992668 cytochrome b-5 363144 0.7924672 transcription factor AP-2 beta (activating enhancer-binding protein 2 beta) 68636 0.7904354 hypothetical protein MGC2477 795185 0.7765346 xenotropic and polytropic retrovirus receptor 255754 0.7720883 LUNX protein; PLUNC (palate lung and nasal epithelium clone); tracheal epithelium enriched protein 767798 0.7682106 ATX1 (antioxidant protein 1, yeast) homolog 1 1558233 0.7654043 ESTs 769600 0.763743 uracil-DNA glycosylase 2 1156538 0.7512287 potassium inwardly-rectifying channel, subfamily J, member 11 1587863 0.7507482 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl- Coenzyme A thiolase) 1709791 0.740832 BAI1-associated protein 1 741891 0.7360507 RAB2, member RAS oncogene family-like 788654 0.7336359 811774 0.7223819 CGI-49 protein 1738208 0.7166687 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4 120138 0.7096046 J domain containing protein 1 2248488 0.7033736 ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate) 265103 0.702883 Homo sapiens mRNA; cDNA DKFZp547M123 (from clone DKFZp547M123) 2054122 0.698129 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3 701751 0.6961443 cut (Drosophila)-like 1 (CCAAT displacement protein) 811582 0.690137 golgi phosphoprotein 2 266312 0.6856592 ATPase, Cu++ transporting, beta polypeptide (Wilson disease) 35147 0.6842172 ESTs, Weakly similar to unnamed protein product [H. sapiens] 1325816 0.6829962 polymerase (RNA) II (DNA directed) polypeptide L (7.6 kD) 358217 0.6801945 glypican 4 233349 0.6764709 hypothetical protein FLJ10761 741977 0.6758385 B-factor, properdin 145132 0.6725186 mannose-P-dolichol utilization defect 1 33267 0.6679827 279720 0.6607182 ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens] 565319 0.6603668 Homo sapiens mRNA; cDNA DKFZp564B1264 (from clone DKFZp564B1264) 771173 0.6594128 mitochondrial ribosomal protein S21 271472 0.6582514 C3HC4-like zinc finger protein 768570 0.6581316 hypothetical protein FLJ11280 744417 0.6563238 carnitine acetyltransferase 826256 0.6554059 transmembrane 7 superfamily member 1 (upregulated in kidney) 2250839 0.654954 androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease) 179212 0.6499845 ESTs, Moderately similar to T12539 hypothetical protein DKFZp434J154.1 [H. sapiens] 785701 0.6496359 RAB31, member RAS oncogene family 186768 0.6495706 Homo sapiens, clone IMAGE: 3604869, mRNA 503215 0.6457259 pilin-like transcription factor 37554 0.6440792 hypothetical protein FLJ22353 2710524 0.6399293 nuclear receptor coactivator 3 284261 0.6398576 uncharacterized hematopoietic stem/progenitor cells protein MDS030 741769 0.6390692 polymerase (DNA directed), beta 743146 0.6388187 hypothetical protein FLJ23403 814528 0.6329458 Homo sapiens cDNA: FLJ22139 fis, clone HEP20959 742595 0.6324947 cyclin-dependent kinase 5 810063 0.630827 growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration) 590310 0.6299822 Homo sapiens mRNA; cDNA DKFZp434E2321 (from clone DKFZp434E2321); partial cds 841679 0.6283163 calcium and integrin binding protein (DNA-dependent protein kinase interacting protein) 131094 0.6268883 Homo sapiens cDNA: FLJ21587 fis, clone COL06946 788334 0.6264069 mitochondrial ribosomal protein L23 1574058 0.6261947 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) 731308 0.6259858 citrate synthase 826194 0.6205287 synaptotagmin-like 2 2110511 0.6203153 artemin 811907 0.6180993 hypothetical protein FLJ22056 814350 0.6173648 insulin-degrading enzyme 611443 0.6112713 myoglobin 782608 0.6105794 22778 0.6100322 sulfortranferase family 4A, member 1 128695 0.608873 ESTs, Weakly similar to I38344 titin, cardiac muscle [H. sapiens] 47853 0.6077928 aldehyde dehydrogenase 4 family, member A1 814209 0.6076904 ESTs 590774 0.6071935 mitogen-activated protein kinase 13 969877 0.6064355 synaptosomal-associated protein, 25 kD 1469425 0.6055267 SRY (sex determining region Y)-box 22 301122 0.6041028 extracellular matrix protein 1 199403 0.6027193 lectin, galactoside-binding, soluble, 8 (galectin 8) 813845 0.6018909 RNA, U transporter 1 810331 0.6014164 quiescin Q6 770766 0.600234 DKFZP564C1940 protein 279970 0.5992634 adenosine A2a receptor 490778 0.5957445 low molecular mass ubiquinone-binding protein (9.5 kD) 288999 0.5955672 small protein effector 1 of Cdc42 504959 0.5953946 Homo sapiens mRNA; cDNA DKFZp586G0321 (from clone DKFZp586G0321) 42408 0.5930231 hypothetical protein MGC4604 263727 0.5926363 DNA segment, single copy probe LNS-CAI/LNS-CAII (deleted in polyposis 854763 0.5918867 Homo sapiens cDNA FLJ11341 fis, clone PLACE1010786 729975 0.5908615 meningioma expressed antigen 5 (hyaluronidase) 1733262 0.5891897 BLu protein 730313 0.5887579 ESTs, Weakly similar to A43932 mucin 2 precursor, intestinal [H. sapiens] 1500000 0.5871787 H2B histone family, member B 595037 0.5870709 retinoic acid induced 3 1635681 0.5859113 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8 kD, B8) 2325804 0.5840656 95 kDa retinoblastoma protein binding protein 2014856 0.5837779 major histocompatibility complex, class I-like sequence 40173 0.5771304 KIAA0807 protein 796723 0.576028 Homo sapiens clone CDABP0014 mRNA sequence 239568 0.5750382 annexin A9 2018527 0.5732092 dolichyl-phosphate mannosyltransferase polypeptide 3 1649374 0.5731982 homogentisate 1,2-dioxygenase (homogentisate oxidase) 809357 0.571929 Bernardinelli-Seip congenital lipodystrophy 2 (seipin) 366132 0.5711651 succinate dehydrogenase complex, subunit C, integral membrane protein, 15 kD 83358 0.5709886 ESTs 1762111 0.5703701 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 244801 0.5693836 Rho guanine exchange factor (GEF) 11 127646 0.5663395 39884 0.5659552 IMP (inosine monophosphate) dehydrogenase 1 202577 0.5629317 histamine N-methyltransferase 588262 0.5614929 Homo sapiens, Similar to RIKEN cDNA 2600001A11 gene, clone MGC: 9907 IMAGE: 3870073, mRNA, complete cds 813419 0.5602324 hydroxyacyl-Coenzyme A dehydrogenase, type II 1911343 0.559091 RAB26, member RAS oncogene family 859761 0.5582503 poliovirus receptor-related 2 (herpesvirus entry mediator B) 342181 0.557997 B-cell CLL/lymphoma 2 1558108 0.5577768 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 2017403 0.5568495 regulator of G-protein signalling 3 122394 0.5554851 guanine nucleotide binding protein (G protein), alpha 15 (Gq class) 824879 0.5548666 hypothetical protein MGC11275 1708055 0.554593 glioblastoma overexpressed 1456701 0.5545861 B-cell CLL/lymphoma 9 186301 0.5537115 Homo sapiens cDNA FLJ12924 fis, clone NT2RP2004709 126851 0.5535041 hypothetical protein FLJ11160 826622 0.5532463 KIAA0430 gene product 151449 0.5503739 protein tyrosine phosphatase, non-receptor type 21 826668 0.550158 KIAA0274 gene product 76605 0.5482232 nesca protein 786072 0.5450231 myosin IC 2244196 0.5432772 B-cell receptor-associated protein BAP29 704414 0.5431136 small nuclear ribonucleoprotein polypeptides B and B1 739578 0.5402953 GPI-anchored metastasis-associated protein homolog 1404774 0.5399447 parathyroid hormone-like hormone 66599 0.5399379 N-acetyltransferase 1 (arylamine N-acetyltransferase) 359250 0.5382989 carbonic anhydrase IV 488202 0.5378254 ESTs, Weakly similar to YZ28_HUMAN HYPOTHETICAL PROTEIN ZAP128 [H. sapiens] 235986 0.5371486 wingless-type MMTV integration site family, member 11 214068 0.5357344 GATA-binding protein 3 1500542 0.5341753 regulator of G-protein signalling 11 470092 0.5319336 like-glycosyltransferase 589115 0.531314 matrix metalloproteinase 1 (interstitial collagenase) 810734 0.5308572 polymerase (DNA-directed), delta 4 685516 0.5304998 putative G protein-coupled receptor 171912 0.5297738 Homo sapiens cDNA FLJ10960 fis, clone PLACE1000564 1858892 0.5295858 hypothetical protein MGC4825 414992 0.5293379 K562 cell-derived leucine-zipper-like protein 1 37708 0.5283276 hypothetical protein MGC3101 713782 0.5273402 a disintegrin and metalloproteinase domain 15 (metargidin) 471568 0.5255851 hematological and neurological expressed 1 812238 0.5237287 hypothetical protein MGC4692 1631735 0.5228778 Homo sapiens, clone IMAGE: 3604336, mRNA, partial cds 74070 0.5225238 endosulfine alpha 782497 0.5218113 Homo sapiens, clone IMAGE: 3010666, mRNA, partial cds 502774 0.5204735 hypothetical protein FLJ20623 1517171 0.5204242 interleukin 2 receptor, alpha 50562 0.5195335 chromosome 8 open reading frame 4 60565 0.5192032 lethal giant larvae (Drosophila) homolog 2 1641894 0.5187462 EST 51083 0.5170561 catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) 296702 0.5164562 deiodinase, iodothyronine, type I 2018337 0.5163293 glucosidase, beta; acid (includes glucosylceramidase) 1605426 0.5150013 hypothetical protein FLJ13352 1474149 0.5138729 poliovirus receptor-related 1 (herpesvirus entry mediator C; nectin) 26294 0.5137265 RNB6 810017 0.5135433 plasminogen activator, urokinase receptor 825822 0.5134094 hypothetical protein 810725 0.51329 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21 kD 781019 0.5132896 paraoxonase 2 726658 0.5132765 non-metastatic cells 3, protein expressed in 1916575 0.5127478 BCL2-interacting killer (apoptosis-inducing) 1469148 0.5125351 FGFR1 oncogene partner 726703 0.5118991 Homo sapiens clone 23736 mRNA sequence 725978 0.5108817 ESTs, Moderately similar to ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 1573946 0.509585 programmed cell death 9 51741 0.5094912 GTP-binding protein 156363 0.5086284 hypothetical protein FLJ12934 177827 0.5085582 synaptotagmin VII 294397 0.505999 DKFZP586A0522 protein 826077 0.503983 pyruvate dehydrogenase (lipoamide) beta 949938 0.5011384 cystatin C (amyloid angiopathy and cerebral hemorrhage) 1957136 0.5006732 phenylethanolamine N-methyltransferase 2018084 0.4999242 Ste-20 related kinase 784140 0.4984039 WD repeat domain 15 810981 0.498146 hypothetical protein FLJ20699 627248 0.4972176 SBBI31 protein 2302099 0.4967769 sialidase 3 (membrane sialidase) 302031 0.49677 Ste20-related serine/threonine kinase 183440 0.4967506 arylsulfatase A 1609748 0.4955206 hypothetical protein MGC10882 183200 0.4955056 fumarylacetoacetate hydrolase (fumarylacetoacetase) 2306697 0.4953741 neuromedin B 292770 0.4944242 Homo sapiens, clone IMAGE: 3627860, mRNA, partial cds 856447 0.494183 interferon, gamma-inducible protein 30 855563 0.4941473 v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 839081 0.4939384 homolog of yeast long chain polyunsaturated fatty acid elongation enzyme 2 49273 0.4937997 solute carrier family 27 (fatty acid transporter), member 4 289505 0.4933344 ESTs, Moderately similar to S65657 alpha-1C-adrenergic receptor splice form 2 [H. sapiens] 782689 0.4930071 solute carrier family 6 (neurotransmitter transporter, creatine), member 8 767495 0.4922026 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 782537 0.490998 Homo sapiens cDNA: FLJ22562 fis, clone HSI01814 855029 0.4904632 Ac-like transposable element 705274 0.4904221 diacylglycerol kinase, delta (130 kD) 202514 0.4902228 DNA (cytosine-5-)-methyltransferase 3 alpha 725649 0.4878638 nuclear factor of activated T-cells, cytoplasmic, calcineurin- dependent 4 1884404 0.4878341 KIAA0285 gene product 825296 0.4858551 low density lipoprotein receptor defect C complementing 839580 0.4826315 ESTs 289857 0.4823282 phenylethanolamine N-methyltransferase 491465 0.4821169 hypothetical protein FLJ10035 360778 0.4820033 261472 0.4814013 putative nuclear protein ORF1-FL49 840768 0.4812559 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16 kD 123614 0.4800042 hypothetical protein MGC4675 1603583 0.4785029 SH3 domain binding glutamic acid-rich protein like 782688 0.4780253 dynein, axonemal, light intermediate polypeptide 784150 0.4763599 RAB31, member RAS oncogene family 770869 0.4762758 hypothetical protein MGC2592 455269 0.4761389 365358 0.4756564 pM5 protein 795256 0.4753832 NPD007 protein 756666 0.474441 protein phosphatase 1, catalytic subunit, alpha isoform 767706 0.4731085 ESTs 488505 0.4727394 accessory proteins BAP31/BAP29 344073 0.4726399 ESTs, Weakly similar to K1CI_HUMAN KERATIN, TYPE I CYTOSKELETAL 9 [H. sapiens] 1558151 0.4723511 basic leucine zipper transcription factor, ATF-like 823615 0.471739 Homo sapiens cDNA: FLJ21245 fis, clone COL01184 49351 0.4697521 SEX gene 1541711 0.4694413 Homo sapiens cDNA: FLJ21513 fis, clone COL05778 868652 0.4682053 complement component 4B 430318 0.4681908 parvalbumin 143426 0.4679928 ras homolog gene family, member B 951125 0.4675003 peroxisomal D3,D2-enoyl-CoA isomerase 66535 0.466705 ornithine decarboxylase antizyme 2 813281 0.4659334 WW domain-containing protein 1 726699 0.4658249 ESTs, Weakly similar to AAB47496 NG5 [H. sapiens] 1492468 0.4643107 DEME-6 protein 1492426 0.4635224 chromosome 19 open reading frame 3 489106 0.4628623 hypothetical protein FLJ11210 488422 0.4626549 high-mobility group 20B 278430 0.4612914 kinesin family member 5C 1518890 0.4610867 metallothionein-like 5, testis-specific (tesmin) 2017756 0.4608709 homolog of yeast MOG1 813631 0.4607567 seven transmembrane protein TM7SF3 1557637 0.4588694 ESTs 298417 0.4587501 trefoil factor 3 (intestinal) 810402 0.4583168 hypothetical protein 767761 0.4565666 DKFZP434B168 protein 1473289 0.4540707 protective protein for beta-galactosidase (galactosialidosis) 773142 0.4530754 hypothetical protein MGC2827 1652310 0.4525789 Homo sapiens, clone MGC: 19613 IMAGE: 3833049, mRNA, complete cds 812143 0.4519186 fibronectin leucine rich transmembrane protein 3 2326057 0.4506179 MLN51 protein 1075635 0.4502629 MLSN1- and TRP-related 825327 0.4497029 Homo sapiens cDNA FLJ14105 fis, clone MAMMA1001202 809838 0.4466933 786545 0.4453714 protein phosphatase 1, regulatory (inhibitor) subunit 3B 183556 0.4452493 gap junction protein, alpha 4, 37 kD (connexin 37) 503889 0.4433034 hypothetical protein FLJ10656 725321 0.44288 estrogen receptor 1 731459 0.4427978 Homo sapiens cDNA: FLJ22296 fis, clone HRC04468 752631 0.4426961 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 1558642 0.4426424 hypothetical protein MGC2771 120271 0.4425879 hypothetical protein MGC4692 487932 0.4419815 synaptotagmin-like 2 1592715 0.4417898 Homer, neuronal immediate early gene, 3 308466 0.4417728 GTP-binding protein Sara 840882 0.441569 nucleotide binding protein 823727 0.4406546 Homo sapiens, clone IMAGE: 2905978, mRNA, partial cds 1636092 0.4404649 hypothetical protein FLJ20657 1505038 0.43988 hypothetical protein FLJ20171 490965 0.4389746 ESTs 346696 0.437234 TEA domain family member 4 345032 0.4360992 ESTs 487733 0.4356439 810612 0.4352602 S100 calcium-binding protein A11 (calgizzarin) 122077 0.434495 putative membrane protein 417801 0.4325892 mitochondrial ribosomal protein L27 878406 0.4311455 metaxin 1 1947381 0.4311314 hypothetical protein FLJ22329 232789 0.4292025 polymerase (RNA) II (DNA directed) polypeptide J (13.3 kD) 809944 0.4291762 KIAA0310 gene product 2019101 0.4289318 angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 8) 1656062 0.4288838 coagulation factor XII (Hageman factor) 1390584 0.4284863 mitochondrial intermediate peptidase 1693357 0.4274493 endothelin 2 75859 −1.6337267 N-myc downstream-regulated gene 2 1558675 −1.4515145 SRY (sex determining region Y)-box 10 753071 −1.4473398 Homo sapiens cDNA: FLJ22528 fis, clone HRC12825 810002 −1.2720931 Homo sapiens, clone MGC: 19762 IMAGE: 3636045, mRNA, complete cds 712139 −1.2371074 ADP-ribosylation factor-like 7 815737 −1.1857965 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle 503671 −1.1528584 Homo sapiens cDNA FLJ14368 fis, clone HEMBA1001122 345670 −1.135654 ESTs, Moderately similar to I59348 CCAAT binding transcription factor CBF subunit C - rat [R. norvegicus] 753038 −1.1168529 kinesin family member C3 741139 −1.1025542 eyes absent (Drosophila) homolog 2 839736 −1.1019142 crystallin, alpha B 2013178 −1.0884449 death associated transcription factor 1 1577736 −1.076549 epidermal growth factor (beta-urogastrone) 788234 −1.0610946 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 150897 −1.0221539 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 757873 −1.0188169 cyclin-dependent kinase 5, regulatory subunit 1 (p35) 291478 −1.0093382 runt-related transcription factor 3 486683 −1.0075654 Homo sapiens mRNA; cDNA DKFZp564J0323 (from clone DKFZp564J0323) 290378 −1.0043647 podocalyxin-like 772913 −0.9823487 calreticulin 544639 −0.9767278 ESTs 814798 −0.9611553 aldehyde dehydrogenase 1 family, member A3 131839 −0.959265 folate receptor 1 (adult) 840266 −0.9425178 Homo sapiens cDNA: FLJ22667 fis, clone HSI08385 1555924 −0.9421074 CSR1 protein 756708 −0.9396531 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 838478 −0.934433 neurocalcin delta 742562 −0.9269494 chromosome 16 open reading frame 5 1469377 −0.9086679 lipoma HMGIC fusion partner-like 2 884462 −0.9065675 Down syndrome critical region gene 1 796542 −0.9052403 ets variant gene 5 (ets-related molecule) 32493 −0.9043423 integrin, alpha 6 284592 −0.9019931 PRO1659 protein 788136 −0.8998648 phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)- homolog phosphodiesterase E4) 1161564 −0.8865787 desmuslin 1635320 −0.8845852 amiloride-sensitive cation channel 2, neuronal 344720 −0.8822302 glycophorin C (Gerbich blood group) 1534700 −0.8804685 KIAA0830 protein 193913 −0.8724313 v-yes-1 Yamaguchi sarcoma viral related oncogene homolog 71087 −0.870641 v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein F 300632 −0.8586688 hypothetical protein FLJ21044 similar to Rbig1 416676 −0.8568853 pellino (Drosophila) homolog 1 69002 −0.8528453 PPAR(gamma) angiopoietin related protein 742685 −0.852598 disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein) 140574 −0.8498606 small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin) 23831 −0.8493217 aldolase C, fructose-bisphosphate 470393 −0.848482 matrix metalloproteinase 7 (matrilysin, uterine) 1474337 −0.844539 phosphorylase, glycogen; brain 753301 −0.8393651 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 51078 −0.8348835 ribosomal protein L44 3172883 −0.8293392 ESTs, Weakly similar to 1709359A dopamine D4 receptor [H. sapiens] 877621 −0.8289253 nGAP-like protein 811920 −0.8286379 interleukin 11 receptor, alpha 156211 −0.8269263 ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58 kD, isoform 1 (Renal tubular acidosis with deafness) 760299 −0.8251086 dickkopf (Xenopus laevis) homolog 3 285377 −0.8214706 pellino (Drosophila) homolog 2 345034 −0.8161772 small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK) 298122 −0.8158372 frizzled (Drosophila) homolog 7 842896 −0.8123068 hypothetical protein DKFZp762L0311 843070 −0.8071984 nucleoporin 88 kD 1257131 −0.8069059 ESTs 796539 −0.803124 KRAB-associated protein 1 139660 −0.79833 ESTs 666879 −0.7950485 annexin A8 200814 −0.7920988 membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) 2016775 −0.7914834 G protein-coupled receptor, family C, group 5, member B 1946448 −0.790849 caveolin 2 1473471 −0.7906678 KIAA0194 protein 1556433 −0.7877792 GRO3 oncogene 1636156 −0.7827089 hypothetical protein FLJ21709 40299 −0.78007 growth differentiation factor 10 1636166 −0.7788972 KIAA0668 protein 1609665 −0.7765472 BarH-like homeobox 2 250797 −0.7739669 hypothetical protein FLJ20038 220395 −0.7687195 hypothetical protein FLJ23293 similar to ARL-6 interacting protein-2 208718 −0.7660278 annexin A1 41869 −0.7646494 hypothetical protein FLJ11017 490023 −0.7621736 hypothetical protein MGC2648 1607229 −0.7562938 tumor protein D52-like 1 133236 −0.7561129 RNA binding motif protein, X chromosome 785733 −0.7554682 hypothetical protein FLJ12892 32489 −0.7521767 hypothetical protein DKFZp566A1524 70201 −0.7513314 mitochondrial solute carrier 611481 −0.7507264 HMG-box transcription factor TCF-3 1554167 −0.7503289 hypothetical protein FLJ14529 768571 −0.7476813 SRY (sex determining region Y)-box 8 783698 −0.7411614 lipin 1 341759 −0.7393558 lung type-I cell membrane-associated glycoprotein 665384 −0.7388404 KIAA1609 protein 142259 −0.7380151 tumor necrosis factor alpha-inducible cellular protein containing leucine zipper domains; Huntingtin interacting protein L; transcrption factor IIIA-interacting protein 810057 −0.7363941 vasoactive intestinal peptide receptor 1 27544 −0.7342174 prominin (mouse)-like 1 739193 −0.7338774 cellular retinoic acid-binding protein 1 813256 −0.7334866 ATP-binding cassette, sub-family B (MDR/TAP), member 1 293964 −0.7275302 butyrophilin, subfamily 3, member A1 272706 −0.7274769 alpha2,3-sialyltransferase 209537 −0.7245778 zinc finger protein 221 67741 −0.7229251 PP2135 protein 823714 −0.7215045 nuclear receptor co-repressor/HDAC3 complex subunit 471196 −0.7192752 integral membrane protein 3 813265 −0.7192289 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 42681 −0.718704 NY-REN-25 antigen 1601845 −0.7178673 Ca2+-promoted Ras inactivator 725152 −0.7173869 hypothetical protein DKFZp762A227 22917 −0.7173328 Homo sapiens mRNA; cDNA DKFZp761M0111 (from clone DKFZp761M0111) 703541 −0.7118124 KIAA1858 protein 529843 −0.7117107 ESTs, Moderately similar to JC5238 galactosylceramide-like protein, GCP [H. sapiens] 377461 −0.7093974 caveolin 1, caveolae protein, 22 kD 1569187 −0.7091259 heparan sulfate (glucosamine) 3-O-sulfotransferase 4 1456118 −0.7074166 proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2) 289760 −0.7058375 ESTs, Highly similar to T00391 hypothetical protein KIAA0612 [H. sapiens] 341774 −0.7044768 major histocompatibility complex, class I, A 75078 −0.7028415 ESTs 505864 −0.7020337 RalGDS-like gene 415191 −0.700303 KIAA0161 gene product 188335 −0.7002579 egf-like module containing, mucin-like, hormone receptor-like sequence 2 132711 −0.6985643 Kruppel-like factor 5 (intestinal) 1864302 −0.6943806 E74-like factor 5 (ets domain transcription factor) 344854 −0.692296 ankyrin repeat domain 3 454970 −0.6853932 DKFZP434G032 protein 79629 −0.6849525 767068 −0.6819032 DKFZP586G1517 protein 378813 −0.679848 secretory leukocyte protease inhibitor (antileukoproteinase) 725076 −0.6798005 5′-nucleotidase (purine), cytosolic type B 491403 −0.6760814 tumor necrosis factor receptor superfamily, member 1B 43764 −0.6743049 hypothetical protein FLJ14033 similar to hypoxia inducible factor 3, alpha subunit 725622 −0.6731681 ESTs 431231 −0.6692022 EGF-containing fibulin-like extracellular matrix protein 2 488956 −0.6682156 CUG triplet repeat, RNA-binding protein 2 72778 −0.6614808 caspase 7, apoptosis-related cysteine protease 360254 −0.6612871 cysteine-rich, angiogenic inducer, 61 76182 −0.6603322 hypothetical protein DKFZp761F241 773487 −0.6598647 hypothetical protein MGC3032 162308 −0.6580605 ESTs 283023 −0.6577611 chemokine (C-X3-C) receptor 1 196992 −0.6573113 aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase) 303109 −0.6571713 purinergic receptor (family A group 5) 897731 −0.6548064 latrophilin 289428 −0.6542789 neurotrophic tyrosine kinase, receptor, type 2 196435 −0.653913 ESTs 504791 −0.6537859 glutathione S-transferase A4 812975 −0.6527728 KIAA0172 protein 488404 −0.6521658 Homo sapiens clone TUA8 Cri-du-chat region mRNA 345056 −0.6490368 KIAA1404 protein 786069 −0.6484842 beta-site APP-cleaving enzyme 48518 −0.6455041 ATP-binding cassette, sub-family A (ABC1), member 5 812048 −0.6438062 prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann- Strausler-Scheinker syndrome, fatal familial insomnia) 868396 −0.6426678 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide 70245 −0.6422928 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 50374 40027 −0.6418674 ESTs 840944 −0.6399619 early growth response 1 809784 −0.6348991 kallikrein 6 (neurosin, zyme) 1881774 −0.6332545 KIAA1678 52419 −0.6326767 Friedreich ataxia region gene X123 120106 −0.631375 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase) 725680 −0.6295778 transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma) 1493218 −0.6292715 hypothetical protein FLJ22297 2018423 −0.6275903 death-associated protein kinase 2 1486082 −0.6241275 heparin-binding growth factor binding protein 868169 −0.6224058 lipoprotein lipase 209137 −0.6161588 gamma-aminobutyric acid (GABA) A receptor, epsilon 248886 −0.6161134 rab3 GTPase-activating protein, non-catalytic subunit (150 kD) 73252 −0.6115602 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) 612274 −0.6108452 tubulin, alpha 1 (testis specific) 346545 −0.6098367 laminin, beta 1 84464 −0.6091345 hypothetical protein FLJ12806 628955 −0.6088522 forkhead box O1A (rhabdomyosarcoma) 490414 −0.6078858 chromosome 2 open reading frame 2 752837 −0.6056177 Homo sapiens mRNA for FLJ00074 protein, partial cds 796904 −0.604755 pleiomorphic adenoma gene-like 1 418159 −0.6038708 synaptogyrin 1 323238 −0.6032171 GRO1 oncogene (melanoma growth stimulating activity, alpha) 1570427 −0.601608 hypothetical protein MGC4309 1500815 −0.6008126 Homo sapiens cDNA: FLJ22130 fis, clone HEP19632 416959 −0.5999728 nuclear factor I/B 782460 −0.5988226 Homo sapiens cDNA FLJ10500 fis, clone NT2RP2000369 824602 −0.5965816 interferon, gamma-inducible protein 16 878798 −0.5956349 beta-2-microglobulin 32299 −0.5945347 inositol(myo)-1(or 4)-monophosphatase 2 277571 −0.59335 KIAA1706 protein 703964 −0.5918604 inositol polyphosphate phosphatase-like 1 796498 −0.5900328 hypothetical protein FLJ14007 504927 −0.5894078 epithelial protein up-regulated in carcinoma, membrane associated protein 17 813520 −0.5889772 EphB3 341763 −0.5868818 caspase 5, apoptosis-related cysteine protease 1856063 −0.5866417 tweety (Drosophila) homolog 1 825356 −0.5850287 Homo sapiens cDNA FLJ11997 fis, clone HEMBB1001458 745011 −0.5836864 Homo sapiens mRNA for KIAA1750 protein, partial cds 812256 −0.5832398 Homo sapiens cDNA: FLJ21693 fis, clone COL09609 2017960 −0.5822336 PP1201 protein 713129 −0.5822078 granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) 815142 −0.5782827 spastic ataxia of Charlevoix-Saguenay (sacsin) 80727 −0.5766546 receptor tyrosine kinase-like orphan receptor 1 45099 −0.5753698 regucalcin (senescence marker protein-30) 415816 −0.5750184 ESTs 306798 −0.5742664 NGFI-A binding protein 1 (EGR1 binding protein 1) 563634 −0.5737239 dendritic cell protein 757191 −0.5735888 ESTs 740620 −0.5730915 tropomyosin 2 (beta) 1470048 −0.5729078 lymphocyte antigen 6 complex, locus E 788518 −0.5724497 peroxisomal membrane protein 3 (35 kD, Zellweger syndrome) 177665 −0.5718286 221846 −0.5714352 checkpoint suppressor 1 37671 −0.5712258 hypothetical protein FLJ21610 2072862 −0.5694163 v-akt murine thymoma viral oncogene homolog 2 132637 −0.5694152 grancalcin, EF-hand calcium-binding protein 1474900 −0.5693091 keratin 15 34093 −0.5692081 EST 1881689 −0.568518 hypothetical protein FLJ20281 1883327 −0.5684295 ESTs 1902764 −0.5683052 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 781017 −0.5676944 early growth response 2 (Krox-20 (Drosophila) homolog) 34150 −0.5673709 ESTs 137602 −0.5667198 Homo sapiens mRNA; cDNA DKFZp434G0972 (from clone DKFZp434G0972) 460126 −0.5652362 KIAA0819 protein 470128 −0.5652125 myosin IE 1880885 −0.5638973 ESTs 811848 −0.5637994 hypothetical protein 1417886 −0.563564 hypothetical protein FLJ23239 756847 −0.5632582 deformed epidermal autoregulatory factor 1 (Drosophila) 505243 −0.5616577 inositol 1,4,5-triphosphate receptor, type 2 840677 −0.5611985 immunoglobulin kappa constant 1911663 −0.5610314 ESTs 66491 −0.5579872 plasmolipin 1420842 −0.5574834 mucosa associated lymphoid tissue lymphoma translocation gene 1 1626996 −0.5573507 c-fos induced growth factor (vascular endothelial growth factor D) 281190 −0.5572026 ESTs 796475 −0.5563457 four and a half LIM domains 3 1870305 −0.5558155 heat shock 27 kD protein 2 767456 −0.5555493 hypothetical protein FLJ22167 292388 −0.554297 795178 −0.5532479 lactate dehydrogenase C 809998 −0.5519459 amylase, alpha 2A; pancreatic 1734754 −0.5512835 hypothetical protein B 27769 −0.5501268 ESTs 950355 −0.550114 ESTs, Weakly similar to S13495 pregnancy zone protein [H. sapiens] 144924 −0.5498123 chromosome 6 open reading frame 5 502436 −0.5489864 insulin receptor substrate 2 138672 −0.5483104 ESTs 160192 −0.5482009 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens] 768007 −0.547374 hypothetical protein 130201 −0.5468031 intercellular adhesion molecule 2 1587847 −0.5466442 minichromosome maintenance deficient (mis5, S. pombe) 6 1558212 −0.5458261 ESTs 1470278 −0.5449844 hypothetical protein FLJ21841 811088 −0.5445374 ephrin-B3 197056 −0.5440514 ESTs 868630 −0.5426831 transforming growth factor beta-stimulated protein TSC-22 530958 −0.5423532 smoothened (Drosophila) homolog 810097 −0.5423072 Homo sapiens cDNA: FLJ21721 fis, clone COLF0381 207735 −0.5422739 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 79254 −0.541673 MHC class I region ORF 85634 −0.5410684 complement component 1, s subcomponent 531319 −0.5404527 serine/threonine kinase 12 754028 −0.5396001 KIAA0469 gene product 470148 −0.5393193 ESTs 35828 −0.5391332 diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor) 970590 −0.5383645 Homo sapiens mRNA; cDNA DKFZp434A115 (from clone DKFZp434A115) 753162 −0.5377767 KIAA0603 gene product 241066 −0.5369493 Homo sapiens cDNA: FLJ21028 fis, clone CAE07155 1909935 −0.5368632 ESTs 153760 −0.5361176 EphB1 247616 −0.5358709 lipoma HMGIC fusion partner 1031640 −0.5354869 ESTs 24958 −0.5349519 Homo sapiens mRNA; cDNA DKFZp434C2016 (from clone DKFZp434C2016) 1686766 −0.5342051 Rag D protein 2009491 −0.5334821 cyclin-E binding protein 1 611532 −0.5320107 troponin I, skeletal, fast 811149 −0.5319742 chromosome 9 open reading frame 3 844703 −0.5309356 Sam68-like phosphotyrosine protein, T-STAR 70749 −0.5295091 Homo sapiens cDNA: FLJ21874 fis, clone HEP02488 324927 −0.5284875 KIAA0375 gene product 491519 −0.5282605 Homo sapiens clone 24775 mRNA sequence 754040 −0.5282144 NS1-associated protein 1 767765 −0.5282008 GTP-binding protein overexpressed in skeletal muscle 2028722 −0.5277252 osteoblast specific factor 2 (fasciclin I-like) 509458 −0.5266016 hypothetical protein from clone 643 360518 −0.5253745 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 40021 −0.5240809 hairless protein (putative single zinc finger transcription factor protein, responsible for autosomal recessive universal congenital alopecia, HR gene) 1901310 −0.5229967 KIAA1209 protein 33949 −0.5222135 phosphoribosyl pyrophosphate synthetase-associated protein 1 814316 −0.521831 ribosomal protein L13 488130 −0.5201845 Homo sapiens cDNA FLJ20767 fis, clone COL06986 462939 −0.5200097 ESTs 770848 −0.5188717 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 245296 −0.5184238 RAD52 (S. cerevisiae) homolog 753034 −0.5182019 nuclear factor I/X (CCAAT-binding transcription factor) 712829 −0.5181236 LIM domain only 2 (rhombotin-like 1) 1577920 −0.5161377 ESTs 814526 −0.5156162 seb4D 773301 −0.5147295 cadherin 3, type 1, P-cadherin (placental) 77972 −0.5144916 complement component 3 1704155 −0.5133015 hypothetical protein SBBI48 1572298 −0.5126426 CD3Z antigen, zeta polypeptide (TiT3 complex) 755689 −0.5122586 retinoic acid receptor, gamma 1876217 −0.5108977 DnaJ (Hsp40) homolog, subfamily A, member 2 712401 −0.5107426 phosphoinositide-3-kinase, catalytic, delta polypeptide 713839 −0.5088558 transcription factor AP-4 (activating enhancer-binding protein 4) 180803 −0.5083354 inositol polyphosphate-1-phosphatase 814443 −0.5075293 hypothetical protein MGC3232

Example V Genes for Discriminating Between Normal and DCIS

As shown in Table 4 below, 1300 genes were identified as being able to discriminate between normal and DCIS. TABLE 4 CloneID Weight Description 1323448 1.397391 cysteine-rich protein 1 (intestinal) 788654 1.2615322 growth factor receptor-bound protein 2 1505038 1.1904802 hypothetical protein FLJ20171 745606 1.1825585 hypothetical protein PP591 565319 1.0969429 Homo sapiens mRNA; cDNA DKFZp564B1264 (from clone DKFZp564B1264) 35147 1.0886084 ESTs, Weakly similar to unnamed protein product [H. sapiens] 178805 1.0274897 Human DNA sequence from clone RP5-850E9 on chromosome 20. Contains part of the gene for a novel C2H2 type zinc finger protein similar to Drosophila Scratch (Scrt), Slug and Xenopus Snail, a novel gene similar to Drosophila CG6762, STSs, GSSs and five CpG 796469 1.0269115 HSPC150 protein similar to ubiquitin-conjugating enzyme 1609836 1.0164283 glutamate-ammonia ligase (glutamine synthase) 366132 1.013995 succinate dehydrogenase complex, subunit C, integral membrane protein, 15 kD 1500000 1.0118809 H2B histone family, member B 812238 1.0043787 hypothetical protein MGC4692 595037 0.990461 retinoic acid induced 3 1554549 0.9764206 hydroxyacyl glutathione hydrolase 488964 0.9569176 H2A histone family, member O 138189 0.9386802 Wolfram syndrome 1 (wolframin) 283919 0.937383 H2A histone family, member L 823598 0.9153521 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 810711 0.9128832 stearoyl-CoA desaturase (delta-9-desaturase) 1911343 0.9116745 RAB26, member RAS oncogene family 503215 0.9108688 pilin-like transcription factor 811774 0.9073627 CGI-49 protein 122077 0.9021901 putative membrane protein 1492238 0.9019233 HSPC003 protein 469686 0.8919992 Ric (Drosophila)-like, expressed in many tissues 685516 0.8762873 putative G protein-coupled receptor 359887 0.8692353 translocase of inner mitochondrial membrane 17 (yeast) homolog A 131094 0.8675719 Homo sapiens cDNA: FLJ21587 fis, clone COL06946 1492463 0.8634521 selenoprotein X, 1 843195 0.8603524 phosphoserine phosphatase 796723 0.8573155 Homo sapiens clone CDABP0014 mRNA sequence 488202 0.8463961 ESTs, Weakly similar to YZ28_HUMAN HYPOTHETICAL PROTEIN ZAP128 [H. sapiens] 1492426 0.8445255 chromosome 19 open reading frame 3 280375 0.8392836 PRO2000 protein 290841 0.8346933 H2B histone family, member A 1917941 0.8340565 purine-rich element binding protein B 1469425 0.8296141 SRY (sex determining region Y)-box 22 2016908 0.8282806 ESTs, Weakly similar to CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR [H. sapiens] 471568 0.8264546 hematological and neurological expressed 1 150003 0.8251408 hypothetical protein FLJ13187 2029173 0.8213721 ESTs, Weakly similar to N-WASP [H. sapiens] 731044 0.8169506 glutaredoxin 2 244801 0.8066357 Rho guanine exchange factor (GEF) 11 2054635 0.7914755 proteasome (prosome, macropain) subunit, alpha type, 7 1605426 0.787298 hypothetical protein FLJ13352 1709791 0.7837549 BAI1-associated protein 1 470061 0.77977 seven in absentia (Drosophila) homolog 2 1640821 0.7790286 ESTs, Weakly similar to I78885 serine/threonine-specific protein kinase [H. sapiens] 199403 0.7754748 lectin, galactoside-binding, soluble, 8 (galectin 8) 741474 0.7732047 glucose phosphate isomerase 1435862 0.7697423 antigen identified by monoclonal antibodies 12E7, F21 and O13 239568 0.767277 annexin A9 841679 0.7666686 calcium and integrin binding protein (DNA-dependent protein kinase interacting protein) 729975 0.7649717 meningioma expressed antigen 5 (hyaluronidase) 2016648 0.7633048 Homo sapiens mRNA; cDNA DKFZp434N1728 (from clone DKFZp434N1728) 2052113 0.7627076 hypothetical protein FLJ10903 347373 0.7563599 transcription elongation factor B (SIII), polypeptide 1 (15 kD, elongin C) 814054 0.7539407 KIAA0040 gene product 741977 0.7538359 B-factor, properdin 272529 0.7486269 phosphomannomutase 2 824879 0.7432221 hypothetical protein MGC11275 122241 0.7394284 proteasome (prosome, macropain) subunit, beta type, 2 744417 0.7356767 carnitine acetyltransferase 868128 0.7347171 JM4 protein 241348 0.7324115 prenylcysteine lyase 509823 0.7304507 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 1636092 0.7270017 hypothetical protein FLJ20657 42408 0.725109 hypothetical protein MGC4604 686552 0.7231319 golgi phosphoprotein 1 898032 0.7216 KIAA0097 gene product 754628 0.7195265 ESTs 826256 0.7190206 transmembrane 7 superfamily member 1 (upregulated in kidney) 2043167 0.7167431 BCL2-associated athanogene 3 827171 0.7154964 ESTs 502774 0.7148695 hypothetical protein FLJ20623 781097 0.7126945 reticulon 3 810725 0.7115051 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21 kD 768570 0.7102463 hypothetical protein FLJ11280 813281 0.7092607 WW domain-containing protein 1 39884 0.7075527 IMP (inosine monophosphate) dehydrogenase 1 969877 0.707469 synaptosomal-associated protein, 25 kD 704254 0.7061648 a disintegrin and metalloproteinase domain 8 236034 0.7039329 uncoupling protein 2 (mitochondrial, proton carrier) 782428 0.701077 KIAA0250 gene product 489351 0.7003616 hypothetical protein DKFZp566J2046 37708 0.6986007 hypothetical protein MGC3101 271472 0.6978431 C3HC4-like zinc finger protein 782608 0.6978285 mitochondrial ribosomal protein L9 704414 0.6940045 small nuclear ribonucleoprotein polypeptides B and B1 288999 0.6938843 small protein effector 1 of Cdc42 51773 0.6925666 hypothetical protein MGC3077 124447 0.6918546 KIAA1184 protein 470099 0.6915952 HT002 protein; hypertension-related calcium-regulated gene 429799 0.6915155 hypothetical protein FLJ21939 similar to 5-azacytidine induced gene 2 1858892 0.6904662 hypothetical protein MGC4825 796694 0.6893307 baculoviral IAP repeat-containing 5 (survivin) 284261 0.6890531 uncharacterized hematopoietic stem/progenitor cells protein MDS030 814528 0.6878182 Homo sapiens cDNA: FLJ22139 fis, clone HEP20959 788654 0.6866898 68636 0.6838604 hypothetical protein MGC2477 308466 0.6800103 GTP-binding protein Sara 1574058 0.6796357 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) 79520 0.6769129 RAB2, member RAS oncogene family 1473289 0.674396 protective protein for beta-galactosidase (galactosialidosis) 365738 0.6740773 ESTs 768064 0.673441 cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1 773922 0.6730903 KIAA0005 gene product 1869201 0.6727191 hypothetical protein MGC2745 686172 0.6724684 KIAA0008 gene product 810558 0.6698194 proteasome (prosome, macropain) 26S subunit, ATPase, 4 753299 0.6694573 hypothetical protein FLJ10504 725454 0.6669973 CDC28 protein kinase 2 470124 0.6641768 RAD1 (S. pombe) homolog 2014034 0.6620303 methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase 209066 0.6611038 859761 0.6573769 poliovirus receptor-related 2 (herpesvirus entry mediator B) 589232 0.6551447 hypothetical protein FLJ11506 340558 0.6550804 actin related protein 2/3 complex, subunit 5 (16 kD) 186768 0.6550741 Homo sapiens, clone IMAGE: 3604869, mRNA 813629 0.6549767 YME1 (S. cerevisiae)-like 1 1492780 0.6544659 Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409 809944 0.6530236 KIAA0310 gene product 83363 0.6526164 protein-L-isoaspartate (D-aspartate) O-methyltransferase 149355 0.6520333 translocating chain-associating membrane protein 752631 0.650399 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 785616 0.6484744 signal sequence receptor, alpha (translocon-associated protein alpha) 76605 0.6484522 nesca protein 742707 0.6476434 ESTs, Weakly similar to MUC2_HUMAN MUCIN 2 PRECURSOR [H. sapiens] 325606 0.647638 hypothetical protein MGC14353 769921 0.6464245 ubiquitin carrier protein E2-C 1435003 0.6457486 tumor suppressing subtransferable candidate 1 1473922 0.6450042 actin related protein 2/3 complex, subunit 3 (21 kD) 1456348 0.6417276 N-acetylneuraminic acid phosphate synthase; sialic acid synthase 1500162 0.6416738 ESTs 1573251 0.6410435 peroxisomal long-chain acyl-coA thioesterase 46248 0.640944 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 49351 0.6386132 SEX gene 824052 0.6375787 chromosome 6 open reading frame 1 1420370 0.6344209 biliverdin reductase B (flavin reductase (NADPH)) 842994 0.6343858 cathepsin Z 810612 0.6341098 S100 calcium-binding protein A11 (calgizzarin) 123614 0.633308 hypothetical protein MGC4675 124781 0.6324418 squalene epoxidase 814378 0.6317382 serine protease inhibitor, Kunitz type, 2 2108077 0.6312583 CGI-112 protein 289978 0.6308861 ubiquitin-like 4 67765 0.6300886 carboxypeptidase M 742595 0.6265846 cyclin-dependent kinase 5 727078 0.6263882 Homo sapiens cDNA: FLJ23602 fis, clone LNG15735 487733 0.6262778 366067 0.625758 cerebellar degeneration-related protein (62 kD) 292770 0.6231261 Homo sapiens, clone IMAGE: 3627860, mRNA, partial cds 366353 0.6203012 DKFZP564C186 protein 810063 0.620086 growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration) 810124 0.6162712 platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29 kD) 713782 0.6149877 a disintegrin and metalloproteinase domain 15 (metargidin) 782608 0.6137782 530197 0.6122721 ESTs, Moderately similar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 44292 0.6122043 Homo sapiens mRNA; cDNA DKFZp434C107 (from clone DKFZp434C107) 2018084 0.6119069 Ste-20 related kinase 789012 0.6104002 fibulin 2 256619 0.6102239 hydroxysteroid (17-beta) dehydrogenase 7 825327 0.6094796 Homo sapiens cDNA FLJ14105 fis, clone MAMMA1001202 842980 0.6081528 developmentally regulated GTP-binding protein 1 811761 0.6045809 Nijmegen breakage syndrome 1 (nibrin) 1601947 0.6045149 cytochrome c oxidase subunit VIIa polypeptide 2 (liver) 1474955 0.6045103 TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68 kD (RNA-binding protein 56) 1758590 0.6040962 fatty-acid-Coenzyme A ligase, long-chain 3 1456701 0.6038789 B-cell CLL/lymphoma 9 207288 0.603346 insulin induced gene 1 1631699 0.6027911 valosin-containing protein 1635681 0.6022549 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8 kD, B8) 768452 0.6018854 Homo sapiens EST from clone 491476, full insert 897806 0.6015789 hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) 108425 0.6008772 770785 0.600311 1,2-alpha-mannosidase IC 2110511 0.5987863 artemin 785795 0.598504 hypothetical protein FLJ12910 120271 0.5982507 hypothetical protein MGC4692 248649 0.5975539 hypothetical protein FLJ13910 2244196 0.5972111 B-cell receptor-associated protein BAP29 66406 0.5966701 hypothetical protein DKFZp762E1312 1537001 0.59528 ESTs 2028949 0.5946445 hypothetical protein PRO1855 40173 0.5940582 KIAA0807 protein 490778 0.5932928 low molecular mass ubiquinone-binding protein (9.5 kD) 503889 0.5930018 hypothetical protein FLJ10656 781019 0.5918462 paraoxonase 2 196189 0.5916252 cytochrome b-5 1734309 0.5894492 sperm associated antigen 4 814350 0.588877 insulin-degrading enzyme 2018821 0.5887114 ATPase inhibitor precursor 365358 0.5883524 pM5 protein 430235 0.5874504 H2B histone family, member Q 1422338 0.5874097 ribonucleotide reductase M2 polypeptide 770845 0.5870877 hexokinase 1 172517 0.5869599 hippocalcin-like 1 1884404 0.5849803 KIAA0285 gene product 625923 0.5839066 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 2322367 0.5832711 reticulon 4 624667 0.5828923 CGI-92 protein 826363 0.5823873 lysophospholipase II 859228 0.5817344 isocitrate dehydrogenase 1 (NADP+), soluble 2302099 0.5813788 sialidase 3 (membrane sialidase) 209066 0.5794211 serine/threonine kinase 15 1844765 0.57783 Homo sapiens mRNA; cDNA DKFZp564O1763 (from clone DKFZp564O1763) 191904 0.5770884 BUB3 (budding uninhibited by benzimidazoles 3, yeast) homolog 951233 0.5767874 proteasome (prosome, macropain) subunit, beta type, 3 809357 0.5767382 Bernardinelli-Seip congenital lipodystrophy 2 (seipin) 825740 0.5762093 DKFZp434J1813 protein 51532 0.5758765 ADP-ribosylation factor-like 6 interacting protein 203003 0.5743416 non-metastatic cells 4, protein expressed in 2015517 0.5742448 hypothetical protein FLJ22237 205049 0.5734444 protein kinase H11; small stress protein-like protein HSP22 752643 0.5732323 group XII secreted phospholipase A2 753400 0.5732322 CGI-204 protein 564847 0.573202 ESTs 785766 0.5731938 hypothetical protein 825585 0.5722829 tubulin-specific chaperone e 37554 0.5706008 hypothetical protein FLJ22353 144880 0.5704416 hypothetical protein from EUROIMAGE 1759349 49273 0.5691181 solute carrier family 27 (fatty acid transporter), member 4 743589 0.568516 ESTs, Weakly similar to T2D3_HUMAN TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT [H. sapiens] 1616253 0.567837 breast carcinoma amplified sequence 1 1581941 0.5676045 hypothetical protein FLJ14540 431505 0.5670119 ESTs, Highly similar to A31026 probable membrane receptor protein [H. sapiens] 2019223 0.5663073 mitochondrial ribosomal protein L17 840878 0.5648009 seladin-1 811024 0.5646461 bone marrow stromal cell antigen 2 564492 0.5626905 mitochondrial carrier homolog 2 725841 0.561197 KIAA0662 gene product 701751 0.561139 cut (Drosophila)-like 1 (CCAAT displacement protein) 767798 0.560181 ATX1 (antioxidant protein 1, yeast) homolog 1 109863 0.559767 epithelial membrane protein 2 1536006 0.5590182 ESTs 1845169 0.5588842 RAB35, member RAS oncogene family 343607 0.5588222 AD-015 protein 212542 0.5587394 Homo sapiens cDNA FLJ12900 fis, clone NT2RP2004321 1700436 0.5569949 ESTs 795256 0.5567908 NPD007 protein 2011515 0.5566484 DKFZP586B0923 protein 504308 0.5564295 hypothetical protein FLJ10540 772925 0.5562164 HSPCO34 protein 469383 0.5558732 chromosome 8 open reading frame 1 810402 0.5555749 hypothetical protein 1409509 0.554703 troponin T1, skeletal, slow 2050827 0.5544641 proteasome (prosome, macropain) 26S subunit, ATPase, 5 770355 0.5518948 lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) 813410 0.5513568 polymerase (RNA) II (DNA directed) polypeptide K (7.0 kD) 80764 0.5510626 hypothetical protein 1631735 0.5502891 Homo sapiens, clone IMAGE: 3604336, mRNA, partial cds 625234 0.550211 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 279970 0.5502099 adenosine A2a receptor 1518402 0.5497179 KIAA1361 protein 753378 0.548977 hypothetical protein FLJ22649 similar to signal peptidase SPC22/23 594500 0.5474088 EST 590774 0.5460342 mitogen-activated protein kinase 13 2055807 0.5460123 protein kinase domains containing protein similar to phosphoprotein C8FW 773188 0.5454398 nuclear receptor subfamily 1, group D, member 2 126851 0.5454014 hypothetical protein FLJ11160 244764 0.5450377 B7 homolog 3 813419 0.5447006 hydroxyacyl-Coenzyme A dehydrogenase, type II 233349 0.5446353 hypothetical protein FLJ10761 785701 0.5446211 RAB31, member RAS oncogene family 268946 0.5440003 WD40 protein Ciao1 611443 0.5432426 myoglobin 510575 0.5430211 hypothetical protein FLJ22087 491465 0.5420241 hypothetical protein FLJ10035 1393018 0.5404243 general transcription factor IIIC, polypeptide 1 (alpha subunit, 220 kD) 785840 0.5401209 SEC24 (S. cerevisiae) related gene family, member D 1460110 0.5392177 proteasome (prosome, macropain) subunit, beta type, 5 731308 0.5371204 citrate synthase 301122 0.5368073 extracellular matrix protein 1 66535 0.5363248 ornithine decarboxylase antizyme 2 265103 0.5361177 Homo sapiens mRNA; cDNA DKFZp547M123 (from clone DKFZp547M123) 788334 0.5347204 mitochondrial ribosomal protein L23 813631 0.534683 seven transmembrane protein TM7SF3 1553306 0.5344506 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 1461477 0.5343834 Homo sapiens mRNA; cDNA DKFZp586I0324 (from clone DKFZp586I0324) 199645 0.5334951 nicastrin 884425 0.5327862 chaperonin containing TCP1, subunit 5 (epsilon) 1518890 0.5314577 metallothionein-like 5, testis-specific (tesmin) 756442 0.5313744 P450 (cytochrome) oxidoreductase 2326057 0.5310995 MLN51 protein 138788 0.5302936 prolactin receptor 1698036 0.5298397 ubiquitin-conjugating enzyme E2 variant 1 811585 0.5288102 huntingtin (Huntington disease) 795185 0.5276861 xenotropic and polytropic retrovirus receptor 629944 0.5273447 myosin VB 784105 0.5259815 ESTs 1696757 0.5254296 hypothetical protein KIAA1165 139835 0.5253386 UDP-glucose dehydrogenase 1738208 0.5240868 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4 593431 0.5235073 ESTs, Moderately similar to CEGT_HUMAN CERAMIDE GLUCOSYLTRANSFERASE [H. sapiens] 2309073 0.5226599 frizzled (Drosophila) homolog 5 825470 0.5218731 topoisomerase (DNA) II alpha (170 kD) 839682 0.5208954 ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13) 1517171 0.5195255 interleukin 2 receptor, alpha 376516 0.5195127 cell division cycle 4-like 774446 0.5181672 adrenomedullin 1476053 0.5179015 RAD51 (S. cerevisiae) homolog (E coli RecA homolog) 489594 0.5178551 hypothetical protein FLJ11565 1573946 0.5173691 programmed cell death 9 503851 0.5170168 nuclear receptor co-repressor/HDAC3 complex subunit 882484 0.5165756 chaperonin containing TCP1, subunit 7 (eta) 51083 0.5162686 catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) 221295 0.5157877 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein 725978 0.5147267 ESTs, Moderately similar to ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 796757 0.5122331 adaptor-related protein complex 3, sigma 1 subunit 150314 0.5114988 lysophospholipase I 302031 0.5111067 Ste20-related serine/threonine kinase 293569 0.5103638 chromosome 1 open reading frame 21 838366 0.5072623 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase (hydroxymethylglutaricaciduria) 122147 0.5067128 120749 0.5060444 ESTs, Moderately similar to KIAA1215 protein [H. sapiens] 855563 0.5059683 v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 487733 0.5057167 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2 (8 kD, AGGG) 625693 0.5055986 hypothetical protein MGC10911 813751 0.5051993 sialyltransferase 4C (beta-galactosidase alpha-2,3- sialytransferase) 842825 0.5047729 G1 to S phase transition 1 323693 0.5047237 adaptor-related protein complex 1, sigma 1 subunit 202514 0.5045411 DNA (cytosine-5-)-methyltransferase 3 alpha 1517749 0.5045134 ESTs 124331 0.5025464 cleavage and polyadenylation specific factor 5, 25 kD subunit 1474424 0.5021308 Homo sapiens cDNA FLJ12758 fis, clone NT2RP2001328 1848977 0.5015371 glycerol kinase 454896 0.5013449 DnaJ (Hsp40) homolog, subfamily A, member 2 1702742 0.5011725 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 746163 0.5009715 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 810734 0.4998276 polymerase (DNA-directed), delta 4 725284 0.4992842 phosphorylase kinase, gamma 2 (testis) 52103 0.4988158 hypothetical protein FLJ23045 739109 0.4986821 adaptor-related protein complex 2, sigma 1 subunit 488505 0.4981852 accessory proteins BAP31/BAP29 365060 0.4976091 RAB11A, member RAS oncogene family 41569 0.4974126 hypothetical protein FLJ12650 81336 0.4955353 uteroglobin 700792 0.4949149 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 1592715 0.4944665 Homer, neuronal immediate early gene, 3 142586 0.4942961 MCT-1 protein 261472 0.4941066 putative nuclear protein ORF1-FL49 246800 0.4927231 hypothetical protein FLJ10803 124298 0.4922937 microsomal glutathione S-transferase 3 1898619 0.4916939 hypothetical protein MGC15737 739126 0.4905859 tissue specific transplantation antigen P35B 376875 0.490328 flavin containing monooxygenase 1 358162 0.4901786 protein predicted by clone 23627 590759 0.4895021 sterol-C4-methyl oxidase-like 1947647 0.4887766 CGI-147 protein 120271 0.4886584 hypothetical protein MGC4692 488642 0.4881613 ESTs, Weakly similar to I38022 hypothetical protein [H. sapiens] 1492468 0.4878466 DEME-6 protein 345538 0.4875796 cathepsin L 344091 0.4871044 ESTs 123441 0.4862068 ribosomal protein L7a 202901 0.48608 vav 2 oncogene 757489 0.4859039 tubulin, alpha 2 49117 0.4856399 KIAA0215 gene product 812994 0.4854155 retinoid X receptor, alpha 731023 0.4853217 WD repeat domain 5 814899 0.4840969 BCL2/adenovirus E1B 19 kD-interacting protein 3-like 756666 0.4835569 protein phosphatase 1, catalytic subunit, alpha isoform 2018337 0.4833207 glucosidase, beta; acid (includes glucosylceramidase) 1568825 0.4829928 Arg/Abl-interacting protein ArgBP2 869375 0.4827093 isocitrate dehydrogenase 2 (NADP+), mitochondrial 595213 0.4824381 hypothetical protein 744374 0.4824256 putative ankyrin-repeat containing protein 73009 0.4822587 ESTs, Weakly similar to A43932 mucin 2 precursor, intestinal [H. sapiens] 70606 0.481356 ESTs 358456 0.4812268 Sec61 gamma 810762 0.4806851 SNARE protein 823930 0.4800704 actin related protein 2/3 complex, subunit 1A (41 kD) 2020898 0.4797032 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 564981 0.4782207 ESTs 1637282 0.4777562 hexokinase 2 855749 0.476968 triosephosphate isomerase 1 744944 0.4769116 myosin VI 263727 0.4767486 DNA segment, single copy probe LNS-CAI/LNS-CAII (deleted in polyposis 470092 0.476018 like-glycosyltransferase 782513 0.4759571 interferon, alpha-inducible protein (clone IFI-6-16) 897813 0.4749348 polyadenylate binding protein-interacting protein 1 141852 0.4748862 purinergic receptor P2Y, G-protein coupled, 2 855800 0.4748367 prolyl endopeptidase 41356 0.4746307 protein phosphatase 2, regulatory subunit B (B56), alpha isoform 753320 0.4744893 hypothetical protein FLJ20533 784140 0.474314 WD repeat domain 15 530310 0.4739401 KIAA0143 protein 813387 0.4727653 diaphorase (NADH/NADPH) (cytochrome b-5 reductase) 358267 0.4719017 EST, Moderately similar to AF119917 63 PRO2831 [H. sapiens] 2018527 0.4717524 dolichyl-phosphate mannosyltransferase polypeptide 3 781342 0.4716127 hypothetical protein MGC11115 785707 0.4708376 protein regulator of cytokinesis 1 140635 0.4706227 ESTs 814306 0.4705205 tumor protein D52 784150 0.4702303 RAB31, member RAS oncogene family 839746 0.4699443 Homo sapiens, Similar to RIKEN cDNA 5830420C20 gene, clone IMAGE: 3633379, mRNA, partial cds 377384 0.4698441 nuclear receptor subfamily 2, group F, member 2 183200 0.4697062 fumarylacetoacetate hydrolase (fumarylacetoacetase) 345423 0.4694596 DKFZP564M112 protein 204686 0.4687565 FXYD domain-containing ion transport regulator 1 (phospholemman) 428582 0.4684705 hypothetical protein FLJ20296 210862 0.4683996 acyl-Coenzyme A oxidase 1, palmitoyl 51741 0.4678807 GTP-binding protein 296702 0.4670993 deiodinase, iodothyronine, type I 840865 0.4666048 myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L) 278531 0.4663008 cytochrome c oxidase subunit VIc 60565 0.4659865 lethal giant larvae (Drosophila) homolog 2 1639531 0.4658349 RAB27A, member RAS oncogene family 346942 0.4657601 phosphatidylinositol glycan, class Q 884498 0.4648731 uncharacterized hypothalamus protein HT012 345787 0.4647372 highly expressed in cancer, rich in leucine heptad repeats 825296 0.4646099 low density lipoprotein receptor defect C complementing 2248488 0.4645687 ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate) 824962 0.4638758 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 843054 0.4637278 KIAA1533 protein 140289 0.4624364 hypothetical protein 1558233 0.4622449 ESTs 265592 0.4615543 activated RNA polymerase II transcription cofactor 4 767761 0.4608709 DKFZP434B168 protein 770766 0.4603527 DKFZP564C1940 protein 814209 0.4602081 ESTs 773674 0.4601667 oncogene TC21 703707 0.4599434 aspartate beta-hydroxylase 951216 0.4594172 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22 kD, PDSW) 139354 0.4582974 hypothetical protein 79710 0.4579008 KIAA0174 gene product 823574 0.457224 endosulfine alpha 845363 0.4570873 non-metastatic cells 1, protein (NM23A) expressed in 283751 0.4567022 cortistatin 810156 0.4561539 deoxythymidylate kinase (thymidylate kinase) 1416782 0.4558415 creatine kinase, brain 810609 0.4551167 hypothetical protein PP1226 770675 0.454729 Homo sapiens cDNA: FLJ21323 fis, clone COL02374 626318 0.4529715 ubinuclein 1 38356 0.4513099 cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase) 705064 0.4497555 transforming, acidic coiled-coil containing protein 3 127646 0.4493747 299815 0.4482635 hypothetical protein DC42 815026 0.4472842 cleavage stimulation factor, 3′ pre-RNA, subunit 3, 77 kD 489823 0.4468978 COX17 (yeast) homolog, cytochrome c oxidase assembly protein 469151 0.4462659 eukaryotic translation initiation factor 2, subunit 2 (beta, 38 kD) 41826 0.4456463 ESTs 47853 0.445149 aldehyde dehydrogenase 4 family, member A1 144740 0.4449229 similar to phosphatidylcholine transfer protein 2 726658 0.4446657 non-metastatic cells 3, protein expressed in 325515 0.444486 hypothetical protein FLJ10980 815781 0.4441245 heat shock 105 kD 746190 0.4430243 hypothetical protein DKFZp761B1514 2016194 0.4417536 glia maturation factor, beta 1584287 0.4413331 KIAA0241 protein 147834 0.4412795 zinc finger protein 217 154610 0.4410751 dynactin 4 754653 0.4405873 cadherin, EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog 742581 0.440367 Homo sapiens cDNA FLJ10366 fis, clone NT2RM2001420 2306987 0.4402912 secreted and transmembrane 1 878406 0.4396935 metaxin 1 430614 0.438809 2,3-bisphosphoglycerate mutase 415102 0.4387892 cell division cycle 25C 358217 0.4385343 glypican 4 1636669 0.4384707 hypothetical protein FLJ21939 similar to 5-azacytidine induced gene 2 83358 0.4380365 ESTs 1325816 0.4379227 polymerase (RNA) II (DNA directed) polypeptide L (7.6 kD) 824524 0.4375695 UDP-galactose transporter related 795805 0.4370764 KIAA0332 protein 743977 0.4368155 Homo sapiens mRNA for TL132 785793 0.4367093 capping protein (actin filament) muscle Z-line, alpha 1 266218 0.4362517 hypothetical protein FLJ11350 769600 0.4362014 uracil-DNA glycosylase 2 1656062 0.4355127 coagulation factor XII (Hageman factor) 2017415 0.43546 centromere protein A (17 kD) 772220 0.4352917 for protein disulfide isomerase-related 811907 0.4340842 hypothetical protein FLJ22056 789376 0.4339171 thioredoxin reductase 1 782503 0.4334388 fatty acid desaturase 1 753897 0.4324066 autocrine motility factor receptor 767289 0.4323485 hypothetical protein FLJ10055 1159963 0.4323117 interferon regulatory factor 7 1652310 0.4321289 Homo sapiens, clone MGC: 19613 IMAGE: 3833049, mRNA, complete cds 358936 0.4314082 ESTs, Weakly similar to T2D3_HUMAN TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT [H. sapiens] 41698 0.4310061 progesterone binding protein 1635665 0.430087 Homo sapiens, RIKEN cDNA 2010100O12 gene, clone MGC: 14813 IMAGE: 4133274, mRNA, complete cds 1558642 0.4298376 hypothetical protein MGC2771 1733262 0.4289711 BLu protein 823694 0.4280476 Homo sapiens chromosome 19, BAC CIT-HSPC_204F22 (BC228680), complete sequence; contains bacterial insertion element 1641894 0.4277815 EST 2572170 0.4277651 ESTs, Weakly similar to T26581 hypothetical protein Y32B12A.3 - Caenorhabditis elegans [C. elegans] 731080 0.4276128 hypothetical protein FLJ12661 649084 0.4275738 carbonic anhydrase XI 795498 0.4270889 putative transmembrane protein 897770 0.4270685 2250839 0.4266248 androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease) 510794 0.4264564 c-myc binding protein 825822 0.4255725 hypothetical protein 825659 0.424655 N-myc downstream regulated 826077 0.4242762 pyruvate dehydrogenase (lipoamide) beta 293727 0.4242722 hypothetical protein MGC861 503866 0.4230404 sperm autoantigenic protein 17 491527 0.4219324 Homo sapiens, Similar to CG7083 gene product, clone MGC: 10534 IMAGE: 3957147, mRNA, complete cds 292936 0.4217115 hypothetical protein FLJ10468 823940 0.4214277 transducer of ERBB2, 1 414992 0.420994 K562 cell-derived leucine-zipper-like protein 1 346134 0.4209894 calcium-regulated heat-stable protein (24 kD) 51657 0.4208387 hypothetical protein ET 2009779 0.420743 rabaptin-5 1523225 0.4195302 oncostatin M receptor 826194 0.4177687 synaptotagmin-like 2 85804 0.4171445 hypothetical protein FLJ21918 725223 0.4167519 KIAA0077 protein 79726 0.4162264 ESTs, Highly similar to T46395 hypothetical protein DKFZp434I1120.1 [H. sapiens] 1762111 0.4160469 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 509588 0.4157059 TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20 kD 327506 0.4152106 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 327506 744047 0.4151137 polo (Drosophia)-like kinase 221499 0.4149929 KIAA0508 protein 745394 0.4147627 Homo sapiens cDNA: FLJ23249 fis, clone COL04196 149539 0.4138942 KIAA1700 823907 0.4135955 hypothetical protein FLJ10511 66317 0.4132405 H1 histone family, member 2 295986 0.413087 emopamil-binding protein (sterol isomerase) 565235 0.4124667 spermine synthase 825386 0.4121622 ATP synthase, H+ transporting, mitochondrial F1F0, subunit d 250313 0.4121296 ESTs 72050 0.4114235 chloride channel, nucleotide-sensitive, 1A 417801 0.4112944 mitochondrial ribosomal protein L27 841501 0.4111707 KIAA0102 gene product 813707 0.410787 regulator of G-protein signalling 16 745083 0.4107735 ubiquitin specific protease 18 244974 0.4105439 hypothetical protein FLJ22875 26883 0.4103824 protein kinase (cAMP-dependent, catalytic) inhibitor beta 280249 0.4096162 Kruppel-like factor 7 (ubiquitous) 74738 0.409593 Homo sapiens, clone IMAGE: 3535294, mRNA, partial cds 1753497 0.409432 ovo (Drosophila) homolog-like 1 204299 0.4073087 replication protein A3 (14 kD) 358609 0.4071867 NADH dehydrogenase (ubiquinone) flavoprotein 3 (10 kD) 290101 0.4071477 ESTs 2306221 0.4068933 wingless-type MMTV integration site family, member 10B 726439 0.4067151 CGI-143 protein 431805 0.405447 granulin 111362 0.4045961 472103 0.4043572 soc-2 (suppressor of clear, C. elegans) homolog 788444 0.4042598 KIAA0033 protein 1632252 0.404193 complement component 1, q subcomponent, alpha polypeptide 150118 0.4039789 hypothetical protein DKFZp434F054 594226 0.403676 Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409 1499828 0.4030396 fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included) 810939 0.40256 hypothetical protein FLJ22169 841621 0.4020253 ESTs, Weakly similar to JE0350 Anterior gradient-2 [H. sapiens] 200144 0.4019827 ring-box 1 486110 0.4017126 profilin 2 292213 0.4014458 guanine nucleotide binding protein (G protein), beta polypeptide 2 1631132 0.401216 peptide transporter 3 669379 0.4011648 Homo sapiens BAC clone RP11-505D17 from 7p22-p21 773685 0.4009493 phosphodiesterase 4D interacting protein (myomegalin) 810411 0.400096 hypothetical protein FLJ13222 1583198 0.39981 ESTs, Weakly similar to S65824 reverse transcriptase homolog [H. sapiens] 84295 0.3989864 interleukin 1 receptor antagonist 757328 0.3985331 hypothetical protein FLJ22678 35626 0.39822 Homo sapiens cDNA FLJ14201 fis, clone NT2RP3002955 1587863 0.3980812 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl- Coenzyme A thiolase) 713862 0.3965573 ubiquitin-protein isopeptide ligase (E3) 343731 0.3962504 43977 0.3961848 KIAA0182 protein 78869 0.3954821 cell membrane glycoprotein, 110000M(r) (surface antigen) 756595 0.395121 S100 calcium-binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11)) 701115 0.3936994 hypothetical protein PRO2013 81599 0.3932769 ubiquitin specific protease 14 (tRNA-guanine transglycosylase) 1636844 0.3926235 ring finger protein 14 703739 0.392298 nuclear cap binding protein subunit 1, 80 kD 279633 0.3907503 ESTs, Highly similar to I38759 zinc finger/leucine zipper protein [H. sapiens] 122091 0.3903482 casein kinase 2, alpha 1 polypeptide 786067 0.390151 cell division cycle 25B 1909574 0.3900357 mitochondrial ribosomal protein S11 263013 0.3894536 procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 491001 0.3884144 glyoxalase I 455275 0.3869874 hypothetical protein FLJ23469 85450 0.3868399 acyl-Coenzyme A oxidase 2, branched chain 773286 0.3861543 solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1 366156 0.3861394 Homo sapiens cDNA FLJ14028 fis, clone HEMBA1003838 49630 0.3858335 calcium channel, voltage-dependent, L type, alpha 1D subunit 121251 0.385792 hypothetical protein MGC5576 2322223 0.3853156 small nuclear ribonucleoprotein polypeptide A 276915 0.3851081 DNA (cytosine-5-)-methyltransferase 3 beta 1591264 0.3849595 transaldolase 1 1434948 0.3849593 HIV TAT specific factor 1 489657 0.3847527 tryptophan rich basic protein 810947 0.3833137 LIS1-interacting protein NUDE1, rat homolog 298417 0.3833014 trefoil factor 3 (intestinal) 154707 0.3831976 MpV17 transgene, murine homolog, glomerulosclerosis 79032 0.3816428 CGI-82 protein 1916575 0.3814206 BCL2-interacting killer (apoptosis-inducing) 1585492 0.3812472 ESTs 1455394 0.3811391 cytochrome c 769942 0.3810371 kinesin-like 4 429387 0.3810004 chimerin (chimaerin) 2 768377 0.3809674 activity-dependent neuroprotective protein 214996 0.380548 ESTs 1557637 0.3805285 ESTs 1517595 0.3804132 KIAA0175 gene product 841260 0.3801713 hypothetical protein 491524 0.3785047 mitochondrial ribosomal protein L13 30170 0.3782337 caspase 3, apoptosis-related cysteine protease 76196 0.3781541 hypothetical protein FLJ20062 2017721 0.3781067 ESTs, Weakly similar to 2109260A B cell growth factor [H. sapiens] 134918 0.3779855 ESTs 347726 0.377767 homeo box D8 1469148 0.3776558 FGFR1 oncogene partner 1649374 0.3771383 homogentisate 1,2-dioxygenase (homogentisate oxidase) 241043 0.3770901 Human clone 137308 mRNA, partial cds 815835 0.3764754 hypothetical protein R33729_1 143426 0.3764075 ras homolog gene family, member B 1412245 0.3762847 carboxypeptidase A2 (pancreatic) 786265 0.3760397 KIAA0750 gene product 266500 0.3758559 ESTs 755301 0.3749416 protein kinase C, delta 294397 0.3744208 DKFZP586A0522 protein 155806 0.3741516 41123 0.3739475 Homo sapiens, Similar to RIKEN cDNA 2210021G21 gene, clone MGC: 14859 IMAGE: 3621871, mRNA, complete cds 454339 0.3738929 thiopurine S-methyltransferase 810316 0.3732635 very long-chain acyl-CoA synthetase; lipidosin 812105 0.3731726 ALL1-fused gene from chromosome 1q 773426 0.3727398 KIAA0391 gene product 1572710 0.3725734 hypothetical protein FLJ21213 772898 0.372064 ribosomal protein S15a 283739 0.3714571 Homo sapiens cDNA FLJ14028 fis, clone HEMBA1003838 289505 0.3714361 ESTs, Moderately similar to S65657 alpha-1C-adrenergic receptor splice form 2 [H. sapiens] 897177 0.3712716 phosphoglycerate mutase 1 (brain) 782547 0.3708058 ESTs 647866 0.3706822 Homo sapiens cDNA FLJ13975 fis, clone Y79AA1001585 1679942 0.3706798 KIAA1053 protein 566443 0.3705134 Homo sapiens cDNA FLJ12793 fis, clone NT2RP2002033 302996 0.3698028 chloride intracellular channel 3 726699 0.3695061 ESTs, Weakly similar to AAB47496 NG5 [H. sapiens] 2094232 0.3693257 chromosome 1 open reading frame 12 2549634 0.3692338 activator of S phase kinase 177827 0.3691459 synaptotagmin VII 852829 0.3691079 karyopherin alpha 3 (importin alpha 4) 207794 0.3679245 nuclear factor (erythroid-derived 2), 45 kD 823909 0.3675927 743810 0.3667087 hypothetical protein MGC2577 810039 0.3662086 defender against cell death 1 53039 0.3659853 carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 809727 0.365892 unc-51 (C. elegans)-like kinase 1 26171 0.3656147 KIAA0856 protein 1570663 0.3656056 FK506-binding protein 4 (59 kD) 179212 0.3649976 ESTs, Moderately similar to T12539 hypothetical protein DKFZp434J154.1 [H. sapiens] 292996 0.36439 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide 259950 0.364359 hypothetical protein FLJ14991 815794 0.3643266 nucleobindin 2 965223 0.3642603 thymidine kinase 1, soluble 592801 0.3638731 serine palmitoyltransferase, long chain base subunit 2 42831 0.3638165 N-terminal kinase-like 788641 0.3638059 adaptor-related protein complex 1, sigma 2 subunit 813845 0.3637519 RNA, U transporter 1 52076 0.3633002 neuroblastoma (nerve tissue) protein 154493 0.3629466 interferon-induced protein 75, 52 kD 1519013 0.3628651 Homo sapiens, clone IMAGE: 3537447, mRNA, partial cds 1434905 0.3624537 homeo box B7 825282 0.3624112 DKFZP586L0724 protein 322617 0.3623149 v-ral simian leukemia viral oncogene homolog B (ras related; GTP binding protein) 814353 0.3622592 phorbol-12-myristate-13-acetate-induced protein 1 2017917 0.360911 Homo sapiens cDNA: FLJ23371 fis, clone HEP16068, highly similar to HSTFIISH Homo sapiens mRNA for transcription elongation factor TFIIS 813616 0.3608471 FK506-binding protein like 1846982 0.3602851 inhibin, beta C 505289 0.3595549 angiotensin II, type I receptor-associated protein 1565079 0.358728 B-cell linker 795401 0.3573481 diacylglycerol O-acyltransferase (mouse) homolog 781047 0.357207 budding uninhibited by benzimidazoles 1 (yeast homolog) 346696 0.3570344 TEA domain family member 4 809466 0.3568464 DNA segment on chromosome 19 (unique) 1177 expressed sequence 743220 0.3566593 hypothetical protein FLJ12517 131268 0.3564734 growth factor receptor-bound protein 14 119133 0.3564449 Homo sapiens mRNA; cDNA DKFZp434B231 (from clone DKFZp434B231) 242706 0.3562469 Homo sapiens, Similar to RIKEN cDNA 5730494N06 gene, clone MGC: 13349 IMAGE: 4249231, mRNA, complete cds 66599 0.3561699 N-acetyltransferase 1 (arylamine N-acetyltransferase) 46716 0.3557556 ESTs 271899 0.355689 Ser-Thr protein kinase related to the myotonic dystrophy protein kinase 25440 0.3554359 staufen (Drosophila, RNA-binding protein) homolog 2 1899312 0.3551595 ESTs 783681 0.354881 upstream regulatory element binding protein 1 131091 0.3548154 Not56 (D. melanogaster)-like protein 300099 0.3547857 ESTs 588436 0.3544892 butyrate-induced transcript 1 2069602 0.3539588 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 810959 0.3534647 Rho GDP dissociation inhibitor (GDI) alpha 649977 0.3534567 Homo sapiens clone CDABP0014 mRNA sequence 345069 0.3532976 nuclear factor (erythroid-derived 2)-like 3 767487 0.3530592 ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1 824943 0.3527414 hypothetical protein 744994 0.3526118 hypothetical protein FLJ12242 773381 0.3525581 N-ethylmaleimide-sensitive factor attachment protein, alpha 1568561 0.3518952 BCL2-like 1 2028916 0.3516982 Homo sapiens mRNA for Hmob33 protein, 3′ untranslated region 753457 0.3515361 NADH dehydrogenase (ubiquinone) Fe—S protein 1 (75 kD) (NADH-coenzyme Q reductase) 2161427 0.3509243 progesterone receptor 1947381 0.3509235 hypothetical protein FLJ22329 82421 0.3506778 zinc finger protein 6 (CMPX1) 504461 0.3506753 opsin 3 (encephalopsin) 754625 0.3503938 ATPase, Class II, type 9A 795543 0.3500184 thioredoxin peroxidase (antioxidant enzyme) 1910316 0.3498986 KIAA0535 gene product 172785 0.3493683 NAG-5 protein 1910078 0.3491481 ESTs, Weakly similar to YK54_YEAST HYPOTHETICAL 18.4 KD PROTEIN IN SIS2-MTD1 INTERGENIC REGION [S. cerevisiae] 321354 0.3489273 mitochondrial ribosomal protein L15 878815 0.3478601 ADP-ribosylation factor 3 741769 0.3475255 polymerase (DNA directed), beta 487831 0.3464379 Homo sapiens cDNA FLJ14059 fis, clone HEMBB1000573 754046 0.3464097 DNA segment on chromosome X (unique) 9879 expressed sequence 344988 0.3464047 530093 0.3463461 myelin protein zero-like 1 823615 0.3462131 Homo sapiens cDNA: FLJ21245 fis, clone COL01184 144881 0.3461767 calumenin 128695 0.3455381 ESTs, Weakly similar to I38344 titin, cardiac muscle [H. sapiens] 884511 0.3440809 cytochrome c oxidase subunit VIIb 128711 0.3437491 anillin (Drosophila Scraps homolog), actin binding protein 470035 0.3436575 prokineticin 1 precursor 1568126 0.3434836 solute carrier family 37 (glycerol-3-phosphate transporter), member 1 588911 0.3427563 2′,5′-oligoadenylate synthetase 1 (40-46 kD) 35191 0.3427094 stromal cell-derived factor 2 814989 0.3426862 protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform 73638 0.3425644 protein tyrosine phosphatase type IVA, member 2 1605178 0.3416196 amino acid transporter system A1 214068 0.3414185 GATA-binding protein 3 755599 0.3413351 interferon induced transmembrane protein 1 (9-27) 782439 0.3413092 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit e 595070 0.3408109 stress-associated endoplasmic reticulum protein 1; ribosome associated membrane protein 4 183440 0.3406314 arylsulfatase A 774502 0.3402891 protein tyrosine phosphatase, non-receptor type 12 235986 0.338857 wingless-type MMTV integration site family, member 11 289936 0.3382708 solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 824108 0.3381616 SCAN domain-containing 1 26617 0.3371923 activated leucocyte cell adhesion molecule 810497 0.3367408 ESTs, Weakly similar to A35363 synapsin I splice form a [H. sapiens] 40042 0.3362557 hypothetical protein FLJ10747 811142 0.3361932 phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta) 2046679 0.3358043 ESTs 487444 0.3357395 cyclic AMP phosphoprotein, 19 kD 78736 0.3354693 Homo sapiens clone 24877 mRNA sequence 1637302 0.3353374 DNAJ domain-containing 825606 0.335057 kinesin-like 1 76362 0.3349202 spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) 1883028 0.3345488 Homo sapiens mRNA; cDNA DKFZp434J1912 (from clone DKFZp434J1912) 789383 0.3341667 cAMP responsive element modulator 302549 0.3340582 basic transcription element binding protein 1 309288 0.334016 replication factor C (activator 1) 4 (37 kD) 712314 0.3338146 myosin regulatory light chain interacting protein 241677 0.3332521 Homo sapiens, clone MGC: 18110 IMAGE: 4152745, mRNA, complete cds 898253 0.3331924 reticulocalbin 2, EF-hand calcium binding domain 770992 0.3331315 81203 0.3328573 paraoxonase 3 416436 0.3325571 mitochondrial ribosomal protein L24 1660666 0.332029 carbonic anhydrase VB, mitochondrial 811582 0.3319191 golgi phosphoprotein 2 2054122 0.3318413 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3 837864 0.3314764 progestin induced protein 1632247 0.3312131 hypothetical protein FLJ23436 298143 0.3307258 ESTs 2027952 0.3307056 hypothetical protein FLJ20297 1600281 0.3304323 nucleolar protein 3 (apoptosis repressor with CARD domain) 814270 0.3300091 polymyositis/scleroderma autoantigen 1 (75 kD) 415589 0.3296266 Homo sapiens clone PP1498 unknown mRNA 1912951 0.329484 uterine-derived 14 kDa protein 726637 0.3292392 t-complex-associated-testis-expressed 1-like 1474684 0.3291536 ephrin-A1 1843843 0.3290269 KIAA1304 protein 266312 0.3289707 ATPase, Cu++ transporting, beta polypeptide (Wilson disease) 135640 0.3288537 syntaxin 3A 279720 0.3282308 ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens] 724888 0.3272422 cytochrome P450, subfamily IVB, polypeptide 1 811808 0.326728 nucleoside diphosphate kinase type 6 (inhibitor of p53-induced apoptosis-alpha) 131566 0.3261265 hypothetical protein MGC11061 154466 0.3258377 STIP1 homology and U-Box containing protein 1 1692195 0.3254467 smg GDS-ASSOCIATED PROTEIN 785368 0.3254362 PDZ-binding kinase; T-cell originated protein kinase 1637516 0.325364 nuclear autoantigen 1637829 0.3246232 ESTs 810567 0.3243984 Homo sapiens, clone MGC: 3182 IMAGE: 3356293, mRNA, complete cds 1027283 0.3242547 ESTs 306806 0.324179 Homo sapiens, Similar to hypothetical protein FLJ12838, clone IMAGE: 4130879, mRNA, partial cds 855406 0.3241172 Homo sapiens clone TCCCIA00176 mRNA sequence 429222 0.3239231 CGI-107 protein 1500542 0.3228485 regulator of G-protein signalling 11 269606 0.3228482 N-methylpurine-DNA glycosylase 74566 0.3226444 exportin 1 (CRM1, yeast, homolog) 754192 0.3225824 Homo sapiens mRNA; cDNA DKFZp586H0924 (from clone DKFZp586H0924) 180785 0.322529 KIAA0726 gene product 824479 0.3225263 exonuclease NEF-sp 842863 0.3225116 N-myc downstream regulated 1708055 0.3225042 glioblastoma overexpressed 1631194 0.3219004 t-complex-associated-testis-expressed 1-like 1 366834 0.3217743 envoplakin 839580 0.3216628 ESTs 245485 0.3215041 hypothetical protein MGC5178 815501 0.3214849 hypothetical protein MGC2721 2017403 0.3211799 regulator of G-protein signalling 3 281476 0.3210873 aspartylglucosaminidase 130835 0.3209345 Homo sapiens, Similar to clone FLB3816, clone IMAGE: 3454380, mRNA 77533 0.3205713 inositol polyphosphate-5-phosphatase, 40 kD 42076 0.3194462 TRK-fused gene 810998 0.3179036 DKFZP434C131 protein 75859 −1.8328232 N-myc downstream-regulated gene 2 760299 −1.7010462 dickkopf (Xenopus laevis) homolog 3 344720 −1.5196431 glycophorin C (Gerbich blood group) 345670 −1.4445337 ESTs, Moderately similar to I59348 CCAAT binding transcription factor CBF subunit C - rat [R. norvegicus] 200814 −1.4325283 membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) 1882697 −1.4318896 peanut (Drosophila)-like 2 1161564 −1.3891189 desmuslin 788234 −1.3761312 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 1558675 −1.3749762 SRY (sex determining region Y)-box 10 285377 −1.3699153 pellino (Drosophila) homolog 2 45099 −1.3515907 regucalcin (senescence marker protein-30) 611532 −1.3158379 troponin I, skeletal, fast 377275 −1.3102234 ataxia-telangiectasia group D-associated protein 810002 −1.3038896 Homo sapiens, clone MGC: 19762 IMAGE: 3636045, mRNA, complete cds 1569187 −1.2971252 heparan sulfate (glucosamine) 3-O-sulfotransferase 4 377461 −1.2798035 caveolin 1, caveolae protein, 22 kD 712139 −1.2738321 ADP-ribosylation factor-like 7 742685 −1.272916 disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein) 811920 −1.2690713 interleukin 11 receptor, alpha 796542 −1.2625621 ets variant gene 5 (ets-related molecule) 486683 −1.2614406 Homo sapiens mRNA; cDNA DKFZp564J0323 (from clone DKFZp564J0323) 753071 −1.2529315 Homo sapiens cDNA: FLJ22528 fis, clone HRC12825 131839 −1.2372478 folate receptor 1 (adult) 300632 −1.2368481 hypothetical protein FLJ21044 similar to Rbig1 839736 −1.2271618 crystallin, alpha B 813265 −1.2230435 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 1469377 −1.2127781 lipoma HMGIC fusion partner-like 2 490023 −1.2114805 hypothetical protein MGC2648 298122 −1.1962478 frizzled (Drosophila) homolog 7 72778 −1.1752838 caspase 7, apoptosis-related cysteine protease 160192 −1.1751869 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens] 22917 −1.1590598 Homo sapiens mRNA; cDNA DKFZp761M0111 (from clone DKFZp761M0111) 877621 −1.1501074 nGAP-like protein 840266 −1.1476896 Homo sapiens cDNA: FLJ22667 fis, clone HSI08385 289760 −1.1390686 ESTs, Highly similar to T00391 hypothetical protein KIAA0612 [H. sapiens] 811848 −1.1350073 hypothetical protein 1556433 −1.1222978 GRO3 oncogene 838478 −1.1175047 neurocalcin delta 1473274 −1.1172693 myosin regulatory light chain 2, smooth muscle isoform 1917449 −1.0894686 serum amyloid A4, constitutive 811088 −1.0851546 ephrin-B3 1554167 −1.0818834 hypothetical protein FLJ14529 67741 −1.0705249 PP2135 protein 2106144 −1.067765 regulated in glioma 2056139 −1.0673271 LIM domain protein 767202 −1.0654145 latent transforming growth factor beta binding protein 2 345034 −1.0600859 small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK) 666879 −1.0463245 annexin A8 130201 −1.0401997 intercellular adhesion molecule 2 878836 −1.037352 secretory granule, neuroendocrine protein 1 (7B2 protein) 52419 −1.0368509 Friedreich ataxia region gene X123 291478 −1.0212528 runt-related transcription factor 3 781014 −1.0161379 suppression of tumorigenicity 5 132857 −1.0084069 Homo sapiens mRNA; cDNA DKFZp586N1323 (from clone DKFZp586N1323) 529843 −1.0036824 ESTs, Moderately similar to JC5238 galactosylceramide-like protein, GCP [H. sapiens] 2504881 −1.000863 signal transducer and activator of transcription 5A 69002 −0.9960916 PPAR(gamma) angiopoietin related protein 841308 −0.9953716 myosin, light polypeptide kinase 488404 −0.9880176 Homo sapiens clone TUA8 Cri-du-chat region mRNA 277571 −0.9841522 KIAA1706 protein 1871116 −0.9821709 Homo sapiens mRNA; cDNA DKFZp434C1714 (from clone DKFZp434C1714); partial cds 897963 −0.9775616 phosphatidic acid phosphatase type 2A 1584540 −0.9754693 Homo sapiens mRNA; cDNA DKFZp586M2022 (from clone DKFZp586M2022) 196435 −0.9665947 ESTs 140574 −0.9652218 small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin) 740620 −0.96496 tropomyosin 2 (beta) 1473471 −0.9623482 KIAA0194 protein 1635320 −0.9586226 amiloride-sensitive cation channel 2, neuronal 416959 −0.957248 nuclear factor I/B 814798 −0.9559895 aldehyde dehydrogenase 1 family, member A3 823871 −0.9429443 SPARC-like 1 (mast9, hevin) 303109 −0.9414602 purinergic receptor (family A group 5) 270826 −0.9389651 Homo sapiens cDNA FLJ13329 fis, clone OVARC1001795 360254 −0.9286811 cysteine-rich, angiogenic inducer, 61 66491 −0.9280245 plasmolipin 814316 −0.9276916 ribosomal protein L13 153760 −0.9227865 EphB1 811149 −0.9216006 chromosome 9 open reading frame 3 786069 −0.9203158 beta-site APP-cleaving enzyme 208718 −0.9190244 annexin A1 416676 −0.9140494 pellino (Drosophila) homolog 1 248631 −0.9106505 aminomethyltransferase (glycine cleavage system protein T) 76182 −0.9106484 hypothetical protein DKFZp761F241 756708 −0.910505 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 712401 −0.9068788 phosphoinositide-3-kinase, catalytic, delta polypeptide 625399 −0.9066615 hypothetical protein similar to beta-transducin family 753038 −0.893161 kinesin family member C3 162308 −0.8910356 ESTs 796181 −0.8888496 growth arrest-specific 6 133236 −0.8888316 RNA binding motif protein, X chromosome 415816 −0.8887425 ESTs 323780 −0.8879854 Homo sapiens cDNA FLJ11177 fis, clone PLACE1007402 1493218 −0.884795 hypothetical protein FLJ22297 1636166 −0.8845211 KIAA0668 protein 1856063 −0.8833091 tweety (Drosophila) homolog 1 34093 −0.8800259 EST 2028722 −0.8800075 osteoblast specific factor 2 (fasciclin I-like) 811837 −0.8764231 eukaryotic translation elongation factor 1 alpha 1 628955 −0.8761473 forkhead box O1A (rhabdomyosarcoma) 884462 −0.8743987 Down syndrome critical region gene 1 306798 −0.8718483 NGFI-A binding protein 1 (EGR1 binding protein 1) 882248 −0.8700731 transgelin 770935 −0.8700104 hypothetical protein FLJ13511 41208 −0.865227 bone morphogenetic protein 1 768571 −0.8572018 SRY (sex determining region Y)-box 8 781017 −0.8526926 early growth response 2 (Krox-20 (Drosophila) homolog) 811837 −0.848137 815737 −0.8444322 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle 814826 −0.8443265 ESTs 767164 −0.842198 ESTs, Weakly similar to MUC2_HUMAN MUCIN 2 PRECURSOR [H. sapiens] 71087 −0.8416951 v-maf musculoaponeurotic fibrosarcoma (avian) oncogene family, protein F 283023 −0.8413949 chemokine (C-X3-C) receptor 1 160609 −0.8405669 ESTs 814443 −0.8385965 hypothetical protein MGC3232 142259 −0.8376566 tumor necrosis factor alpha-inducible cellular protein containing leucine zipper domains; Huntingtin interacting protein L; transcrption factor IIIA-interacting protein 990881 −0.8335353 970590 −0.8333968 Homo sapiens mRNA; cDNA DKFZp434A115 (from clone DKFZp434A115) 470393 −0.830751 matrix metalloproteinase 7 (matrilysin, uterine) 772913 −0.8306579 calreticulin 741139 −0.8299902 eyes absent (Drosophila) homolog 2 27769 −0.8298821 ESTs 544639 −0.8275232 ESTs 1587710 −0.8252065 period (Drosophila) homolog 1 757191 −0.8247438 ESTs 80344 −0.8243418 interleukin 7 receptor 1635062 −0.8243024 DKFZP586A011 protein 119290 −0.8224756 cortic al thymocyte receptor (X. laevis CTX) like 161456 −0.8215502 serum amyloid A1 1909935 −0.8169271 ESTs 1257131 −0.8163443 ESTs 868396 −0.808677 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide 1609665 −0.8086161 BarH-like homeobox 2 2016775 −0.8063264 G protein-coupled receptor, family C, group 5, member B 796475 −0.8041136 four and a half LIM domains 3 1555924 −0.8025163 CSR1 protein 416434 −0.8006527 SCN Circadian Oscillatory Protein (SCOP) 322561 −0.7970805 ribosomal protein L31 132711 −0.7962294 Kruppel-like factor 5 (intestinal) 70245 −0.795375 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 50374 283124 −0.7933772 ESTs, Moderately similar to LONG-CHAIN FATTY ACID TRANSPORT PROTEIN [M. musculus] 281190 −0.7927001 ESTs 250883 −0.7925068 ubiquitin-activating enzyme E1-like 346545 −0.7887371 laminin, beta 1 1878409 −0.7869766 catechol-O-methyltransferase 530958 −0.7809384 smoothened (Drosophila) homolog 40027 −0.7779473 ESTs 788136 −0.7778375 phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)- homolog phosphodiesterase E4) 1626304 −0.7769866 spinal cord-derived growth factor-B 1474337 −0.7766266 phosphorylase, glycogen; brain 85840 −0.7754435 nicotinamide N-methyltransferase 290378 −0.7751825 podocalyxin-like 2243051 −0.7736287 kallikrein 8 (neuropsin/ovasin) 813256 −0.7731864 ATP-binding cassette, sub-family B (MDR/TAP), member 1 47043 −0.7729643 tensin 343695 −0.7706809 hypothetical protein FLJ10875 491403 −0.7700599 tumor necrosis factor receptor superfamily, member 1B 767765 −0.7691523 GTP-binding protein overexpressed in skeletal muscle 681992 −0.7691299 Homo sapiens cDNA FLJ13384 fis, clone PLACE1001062, highly similar to Homo sapiens mRNA for lysine-ketoglutarate reductase/saccharopine dehydrogenase 505864 −0.7677235 RalGDS-like gene 139660 −0.7677153 ESTs 869450 −0.7659922 ribosomal protein L11 162308 −0.7654139 209537 −0.763749 zinc finger protein 221 753162 −0.7617972 KIAA0603 gene product 810728 −0.7607171 hypothetical gene ZD52F10 366591 −0.7595643 T-cell lymphoma invasion and metastasis 2 488258 −0.7574184 collagen, type XVI, alpha 1 32489 −0.7571259 hypothetical protein DKFZp566A1524 1519147 −0.7548183 418159 −0.7545888 synaptogyrin 1 80727 −0.7538606 receptor tyrosine kinase-like orphan receptor 1 593023 −0.7516846 dystrobrevin, beta 586803 −0.7423407 placental growth factor, vascular endothelial growth factor- related protein 188335 −0.7399294 egf-like module containing, mucin-like, hormone receptor-like sequence 2 1161775 −0.7380353 villin 1 490668 −0.7364434 Homo sapiens mRNA; cDNA DKFZp586B211 (from clone DKFZp586B211) 1474900 −0.736252 keratin 15 378813 −0.7346408 secretory leukocyte protease inhibitor (antileukoproteinase) 1630990 −0.7312981 ribosomal protein L29 280907 −0.7307519 Kruppel-type zinc finger protein 742562 −0.730047 chromosome 16 open reading frame 5 73252 −0.7283898 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) 26566 −0.7278186 protein-O-mannosyltransferase 1 1471829 −0.7275378 uncharacterized hypothalamus protein HSMNP1 289428 −0.7270494 neurotrophic tyrosine kinase, receptor, type 2 898092 −0.7267434 connective tissue growth factor 34150 −0.7263513 ESTs 24958 −0.7225195 Homo sapiens mRNA; cDNA DKFZp434C2016 (from clone DKFZp434C2016) 725680 −0.7197488 transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma) 77972 −0.7194713 complement component 3 1686766 −0.7192745 Rag D protein 471196 −0.7192268 integral membrane protein 3 431231 −0.7182897 EGF-containing fibulin-like extracellular matrix protein 2 1908834 −0.7177051 ubiquitin A-52 residue ribosomal protein fusion product 1 207735 −0.7167416 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 754157 −0.7165332 Homo sapiens mRNA; cDNA DKFZp434K2172 (from clone DKFZp434K2172) 35828 −0.7163689 diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor) 1946448 −0.7150027 caveolin 2 470148 −0.712917 ESTs 840944 −0.7099353 early growth response 1 809784 −0.7095414 kallikrein 6 (neurosin, zyme) 877827 −0.7093855 ribosomal protein S27a 32493 −0.7093777 integrin, alpha 6 813520 −0.7092422 EphB3 782501 −0.7086066 hypothetical protein PP1665 27544 −0.708383 prominin (mouse)-like 1 184022 −0.7070266 amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65) 323238 −0.7042807 GRO1 oncogene (melanoma growth stimulating activity, alpha) 488956 −0.70192 CUG triplet repeat, RNA-binding protein 2 1926246 −0.701769 ESTs, Moderately similar to T46371 hypothetical protein DKFZp434P1018.1 [H. sapiens] 325365 −0.7012106 HIV-1 rev binding protein 2 221846 −0.6982802 checkpoint suppressor 1 1870305 −0.6958213 heat shock 27 kD protein 2 277044 −0.6947855 KIAA1183 protein 503335 −0.6944661 hypothetical protein FLJ11196 757873 −0.6940266 cyclin-dependent kinase 5, regulatory subunit 1 (p35) 2306682 −0.6934667 A kinase (PRKA) anchor protein (yotiao) 9 1864302 −0.6932327 E74-like factor 5 (ets domain transcription factor) 843070 −0.6925728 nucleoporin 88 kD 812975 −0.6921755 KIAA0172 protein 46129 −0.6919169 ESTs, Highly similar to T17245 hypothetical protein DKFZp586J0917.1 [H. sapiens] 270917 −0.6918383 secreted frizzled-related protein 1 789382 −0.6898974 Notch (Drosophila) homolog 4 611481 −0.6894079 HMG-box transcription factor TCF-3 35300 −0.688788 KIAA0869 protein 50892 −0.6887497 Homo sapiens, clone MGC: 9913 IMAGE: 3870821, mRNA, complete cds 366100 −0.6885372 matrilin 2 345056 −0.6863529 KIAA1404 protein 2783721 −0.6854649 cholinergic receptor, nicotinic, beta polypeptide 1 (muscle) 178137 −0.6839022 ribosomal protein L34 1626996 −0.682449 c-fos induced growth factor (vascular endothelial growth factor D) 188388 −0.6824191 integrin, alpha 10 133518 −0.6817662 microtubule-associated protein, RP/EB family, member 2 839796 −0.6807912 candidate tumor suppressor p33 ING1 homolog 726582 −0.6807781 actin-related protein 3-beta 50586 −0.6794282 KIAA1545 protein 491763 −0.679034 interleukin 1, beta 52096 −0.6789228 platelet-derived growth factor receptor, alpha polypeptide 263716 −0.6767498 collagen, type VI, alpha 1 2095066 −0.676021 alcohol dehydrogenase 1C (class I), gamma polypeptide 1475738 −0.6753091 ribosomal protein S25 41869 −0.6747514 hypothetical protein FLJ11017 1350439 −0.6740833 KIAA0015 gene product 502689 −0.6739476 Homo sapiens clone HH409 unknown mRNA 773373 −0.6730112 hypothetical protein MGC14258 308539 −0.6726187 Homo sapiens cDNA FLJ12777 fis, clone NT2RP2001720 343760 −0.6724144 SH3 domain binding glutamic acid-rich protein like 2 769959 −0.6720196 collagen, type IV, alpha 2 2252954 −0.6687686 enhancer of filamentation 1 (cas-like docking; Crk-associated substrate related) 70201 −0.6675012 mitochondrial solute carrier 505243 −0.6671218 inositol 1,4,5-triphosphate receptor, type 2 897731 −0.6670507 latrophilin 296880 −0.6655878 membrane protein, palmitoylated 1 (55 kD) 1486082 −0.6635259 heparin-binding growth factor binding protein 1470278 −0.6633411 hypothetical protein FLJ21841 177665 −0.6624986 725152 −0.6591675 hypothetical protein DKFZp762A227 247616 −0.6585351 lipoma HMGIC fusion partner 752668 −0.65723 KIAA0440 protein 837870 −0.657186 proline arginine-rich end leucine-rich repeat protein 744918 −0.6552361 Homo sapiens mRNA; cDNA DKFZp761I0911 (from clone DKFZp761I0911) 39600 −0.6540275 adenylate kinase 5 795288 −0.6528792 ubiquitin specific protease 4 (proto-oncogene) 1665444 −0.651994 tumor endothelial marker 1 precursor 774078 −0.6508021 leiomodin 1 (smooth muscle) 415233 −0.6506593 ribosomal protein L37a 307029 −0.6500872 ribosomal protein L26 78946 −0.648366 Homo sapiens pyruvate dehydrogenase kinase 4 mRNA, 3′ untranslated region, partial sequence 785733 −0.6476493 hypothetical protein FLJ12892 415415 −0.646492 EST, Moderately similar to RL1X_HUMAN 60S RIBOSOMAL PROTEIN L18A [H. sapiens] 858167 −0.6453859 fatty-acid-Coenzyme A ligase, long-chain 4 823714 −0.642903 nuclear receptor co-repressor/HDAC3 complex subunit 193913 −0.6425581 v-yes-1 Yamaguchi sarcoma viral related oncogene homolog 220395 −0.6418175 hypothetical protein FLJ23293 similar to ARL-6 interacting protein-2 840942 −0.6383764 major histocompatibility complex, class II, DP beta 1 725308 −0.6371261 ras inhibitor 1492147 −0.636656 ribosomal protein S4, X-linked 1466893 −0.6364598 ESTs 75078 −0.6362307 ESTs 796152 −0.6356106 Homo sapiens cDNA FLJ11685 fis, clone HEMBA1004934 190059 −0.634814 guanine nucleotide binding protein (G protein), gamma 7 840511 −0.6341661 vimentin 81409 −0.6338327 GABA(A) receptor-associated protein like 1 745490 −0.6329354 hypothetical protein FLJ20607 530036 −0.6324794 hypothetical protein FLJ13078 755855 −0.6298333 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 785538 −0.6289951 Homo sapiens mRNA; cDNA DKFZp434N2116 (from clone DKFZp434N2116) 2284803 −0.6265431 secretory carrier membrane protein 1 1623016 −0.6263561 EST 154472 −0.6253276 fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) 774754 −0.6243946 catenin (cadherin-associated protein), beta 1 (88 kD) 1572298 −0.6228686 CD3Z antigen, zeta polypeptide (TiT3 complex) 2252417 −0.6222381 ribosomal protein S10 180803 −0.621787 inositol polyphosphate-1-phosphatase 683059 −0.6216483 Cdc42 effector protein 3 1577736 −0.6215965 epidermal growth factor (beta-urogastrone) 241489 −0.6212938 adrenergic, beta-2-, receptor, surface 2316441 −0.6206597 ras homolog gene family, member C 1712825 −0.6204409 ESTs 52724 −0.6199204 hypothetical protein FLJ20241 150897 −0.6188264 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 3 823851 −0.6182341 AE-binding protein 1 810057 −0.6178096 vasoactive intestinal peptide receptor 1 81316 −0.6176265 ESTs 298134 −0.6152731 frizzled (Drosophila) homolog 1 2028238 −0.6141182 KIAA0300 protein 1898758 −0.6126872 BCE-1 protein 250797 −0.6124667 hypothetical protein FLJ20038 754040 −0.610807 NS1-associated protein 1 1584628 −0.6102937 alpha-actinin-2-associated LIM protein 230910 −0.6096107 172783 −0.6088873 hypothetical protein FLJ10390 824799 −0.6054867 ART-4 protein 785967 −0.6049171 erythrocyte membrane protein band 4.1-like 2 342349 −0.603487 mitogen-activated protein kinase kinase kinase 14 67067 −0.6003961 Homo sapiens mRNA; cDNA DKFZp564O222 (from clone DKFZp564O222) 1533710 −0.5988282 ortholog of mouse integral membrane glycoprotein LIG-1 768007 −0.5983563 hypothetical protein 1707637 −0.5964339 ESTs 1634832 −0.5931096 class I cytokine receptor 1609625 −0.5920312 selectin P ligand 1592530 −0.5918818 mammalian inositol hexakisphosphate kinase 2 272706 −0.5914377 alpha2,3-sialyltransferase 897720 −0.5904719 trophinin 1472735 −0.5888169 metallothionein 1E (functional) 767641 −0.5881449 mitogen-activated protein kinase 8 interacting protein 2 1651906 −0.5863631 hypothetical protein FLJ23544 564801 −0.5824549 Homo sapiens cDNA: FLJ21409 fis, clone COL03924 248886 −0.5823315 rab3 GTPase-activating protein, non-catalytic subunit (150 kD) 250654 −0.5815576 secreted protein, acidic, cysteine-rich (osteonectin) 1968422 −0.5802058 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1968422 712829 −0.5797871 LIM domain only 2 (rhombotin-like 1) 752837 −0.5794612 Homo sapiens mRNA for FLJ00074 protein, partial cds 346902 −0.5794362 ESTs, Weakly similar to ALU2_HUMAN ALU SUBFAMILY SB SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 782193 −0.5788147 thioredoxin 358531 −0.5784457 v-jun avian sarcoma virus 17 oncogene homolog 2271240 −0.5782432 hypothetical protein 66532 −0.5773248 endothelin 3 120106 −0.5770131 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase) 810552 −0.5768989 B-cell associated protein 770848 −0.5767154 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 1032831 −0.5764161 gycosyltransferase 460403 −0.5739604 laminin, gamma 2 (nicein (100 kD), kalinin (105 kD), BM600 (100 kD), Herlitz junctional epidermolysis bullosa)) 489755 −0.5730453 a disintegrin and metalloproteinase domain 12 (meltrin alpha) 502753 −0.5724623 angiopoietin 2 68534 −0.5724394 Homo sapiens cDNA: FLJ22290 fis, clone HRC04405 854645 −0.5723062 CDC-like kinase 3 322024 −0.5714933 ESTs, Highly similar to T12495 hypothetical protein DKFZp434H071.1 [H. sapiens] 140071 −0.5708303 frizzled-related protein 788518 −0.5697316 peroxisomal membrane protein 3 (35 kD, Zellweger syndrome) 240752 −0.56913 hypothetical protein MGC14797 773487 −0.5686324 hypothetical protein MGC3032 1404774 −0.5685596 parathyroid hormone-like hormone 814815 −0.5675649 plakophilin 4 462939 −0.5662456 ESTs 240248 −0.5660209 transferrin 208001 −0.5640857 CD59 antigen p18-20 (antigen identified by monoclonal antibodies 16.3A5, EJ16, EJ30, EL32 and G344) 1909433 −0.5638242 DKFZP727C091 protein 1636360 −0.5629882 hypothetical protein FLJ14957 138242 −0.5621088 ESTs, Moderately similar to MAS2_HUMAN MANNAN- BINDING LECTIN SERINE PROTEASE 2 PRECURSOR [H. sapiens] 703964 −0.5620699 inositol polyphosphate phosphatase-like 1 1522734 −0.5618289 ESTs 843094 −0.5617478 ubiquitin-like 1 (sentrin) 491519 −0.561401 Homo sapiens clone 24775 mRNA sequence 377314 −0.561312 casein kinase 2, alpha prime polypeptide 208969 −0.561267 EST 788558 −0.5600825 KIAA1479 protein 785530 −0.5600048 integrin, alpha 1 1473131 −0.5594101 transducin-like enhancer of split 2, homolog of Drosophila E(sp1) 812959 −0.5591846 KIAA1638 protein 868169 −0.5584677 lipoprotein lipase 322233 −0.5578912 ribosomal protein, large, P0 50519 −0.5577761 aryl hydrocarbon receptor nuclear translocator-like 299720 −0.5565137 215000 −0.555725 vasoactive intestinal peptide receptor 1 51981 −0.5554908 ribosomal protein L7a 703541 −0.5534921 KIAA1858 protein 238907 −0.5534598 hypothetical protein, clone Telethon(Italy_B41)_Strait02270_FL142 415613 −0.5528761 DHHC1 protein 282404 −0.5528532 Homo sapiens mRNA for KIAA1671 protein, partial cds 344588 −0.55146 kallikrein 5 746373 −0.5513143 RNA polymerase I transcription factor RRN3 491186 −0.5507413 Homo sapiens cDNA: FLJ23131 fis, clone LNG08502 75059 −0.5504962 poly(A)-binding protein, cytoplasmic 1-like 345764 −0.5504113 special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA's) 1577920 −0.5496944 ESTs 288748 −0.5493871 Homo sapiens, clone MGC: 5352 IMAGE: 3048106, mRNA, complete cds 810097 −0.5487174 Homo sapiens cDNA: FLJ21721 fis, clone COLF0381 755881 −0.5473964 aquaporin 5 1568391 −0.5467858 plastin 3 (T isoform) 290866 −0.5467613 v-raf-1 murine leukemia viral oncogene homolog 1 503671 −0.5461871 Homo sapiens cDNA FLJ14368 fis, clone HEMBA1001122 2388571 −0.5459823 A kinase (PRKA) anchor protein 8 739193 −0.5457998 cellular retinoic acid-binding protein 1 756372 −0.5447652 retinoic acid receptor responder (tazarotene induced) 2 53081 −0.5446617 ESTs 486179 −0.5443525 Homo sapiens cDNA FLJ10205 fis, clone HEMBA1004954 84464 −0.5426397 hypothetical protein FLJ12806 2213824 −0.5412089 protease inhibitor 3, skin-derived (SKALP) 1597813 −0.5406089 hypothetical protein PP1044 810358 −0.5403705 acyl-Coenzyme A dehydrogenase, very long chain 341759 −0.5403406 lung type-I cell membrane-associated glycoprotein 309449 −0.5401954 ribosomal protein S4, Y-linked 42681 −0.5388424 NY-REN-25 antigen 299720 −0.5388238 eukaryotic translation elongation factor 1 alpha 1 162775 −0.5385174 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68 kD) 490102 −0.5383385 TBP-associated factor 172 877835 −0.5382125 ribosomal protein L35 299720 −0.5378801 eukaryotic translation elongation factor 1 alpha 1 1534493 −0.5376323 ESTs 595637 −0.5373697 Homo sapiens mRNA; cDNA DKFZp586N012 (from clone DKFZp586N012) 725622 −0.5370309 ESTs 233679 −0.5356625 hypothetical protein FLJ22362 785933 −0.5340762 sushi-repeat-containing protein, X chromosome 825356 −0.533771 Homo sapiens cDNA FLJ11997 fis, clone HEMBB1001458 767982 −0.533231 Homo sapiens, clone IMAGE: 4134852, mRNA, partial cds 277627 −0.5329107 Human SH3 domain-containing protein SH3P18 mRNA, complete cds 460126 −0.5320146 KIAA0819 protein 346688 −0.5315035 melanoma inhibitory activity 712023 −0.5302372 AT-binding transcription factor 1 24729 −0.5302207 cholinergic receptor, muscarinic 1 1590021 −0.5302114 ets variant gene 6 (TEL oncogene) 809998 −0.5297152 811779 −0.5291718 phosphoinositide-3-kinase, regulatory subunit, polypeptide 1 (p85 alpha) 488130 −0.5289721 Homo sapiens cDNA FLJ20767 fis, clone COL06986 299720 −0.5284407 159462 −0.528299 serum constituent protein 1570427 −0.5280955 hypothetical protein MGC4309 2308346 −0.5268833 cyclin-dependent kinase 2 1881774 −0.5265891 KIAA1678 591055 −0.5258289 protein kinase C and casein kinase substrate in neurons 2 470128 −0.5253542 myosin IE 687990 −0.5253354 Rac/Cdc42 guanine exchange factor (GEF) 6 753620 −0.5248489 insulin-like growth factor binding protein 6 80374 −0.5236475 pyruvate dehydrogenase (lipoamide) alpha 1 878421 −0.5233873 transgelin 2 343079 −0.5224833 Homo sapiens mRNA; cDNA DKFZp761P0114 (from clone DKFZp761P0114) 284592 −0.5205573 PRO1659 protein 855061 −0.5203046 vascular endothelial growth factor B 183704 −0.5184644 Homo sapiens, clone MGC: 13446 IMAGE: 4275731, mRNA, complete cds 155896 −0.5182247 ORF 842939 −0.5172329 adenosine deaminase, RNA-specific, B1 (homolog of rat RED1) 685185 −0.5172158 reticulon 2 753301 −0.5171758 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 795178 −0.5169102 lactate dehydrogenase C 1911663 −0.5168962 ESTs 345023 −0.5166203 ESTs, Highly similar to T08701 hypothetical protein DKFZp564N123.1 [H. sapiens] 1631682 −0.5162406 peptidylprolyl isomerase E (cyclophilin E) 868308 −0.5157133 ribosomal protein S23 809998 −0.5144681 amylase, alpha 2A; pancreatic 771004 −0.5144276 KIAA1201 protein 842896 −0.5137089 hypothetical protein DKFZp762L0311 714213 −0.5129593 tumor necrosis factor receptor superfamily, member 6 197056 −0.5128128 ESTs 415191 −0.512457 KIAA0161 gene product 2306752 −0.5123647 stathmin-like 2 469306 −0.5113377 gastrin-releasing peptide 824602 −0.5107682 interferon, gamma-inducible protein 16 307687 −0.5106552 protease, serine, 16 (thymus) 1637296 −0.5105214 ribosomal protein S24 1358393 −0.5090372 mitogen-activated protein kinase kinase 3 504940 −0.508056 713839 −0.5080365 transcription factor AP-4 (activating enhancer-binding protein 4) 220293 −0.5078291 Homo sapiens cDNA: FLJ21800 fis, clone HEP00618 125342 −0.5078237 SUMO-1-specific protease 1601845 −0.5074894 Ca2+-promoted Ras inactivator 240620 −0.5065007 vascular Rab-GAP/TBC-containing 43679 −0.5063146 ESTs 825013 −0.505654 acidic protein rich in leucines 2116188 −0.5046972 histone deacetylase 5 161998 −0.5044691 hypothetical protein FLJ23138 83999 −0.5044612 Human DNA sequence from clone 889N15 on chromosome Xq22.1-22.3. Contains part of the gene for a novel protein similar to X. laevis Cortical Thymocyte Marker CTX, the possibly alternatively spliced gene for 26S Proteasome subunit p28 (Ankyrin repeat prote 593840 −0.5033966 DKFZP564K1964 protein 51448 −0.5031992 activating transcription factor 3 383501 −0.502319 regulator of G-protein signalling 9 2018423 −0.501705 death-associated protein kinase 2 796984 −0.5010588 cytochrome b-245, beta polypeptide (chronic granulomatous disease) 1160723 −0.5005952 LIM domain kinase 2 414999 −0.5002542 ets variant gene 4 (E1A enhancer-binding protein, E1AF) 770212 −0.4981295 chitinase 3-like 1 (cartilage glycoprotein-39) 48518 −0.4966991 ATP-binding cassette, sub-family A (ABC1), member 5 85634 −0.4961026 complement component 1, s subcomponent 341763 −0.4953701 caspase 5, apoptosis-related cysteine protease 812161 −0.4948424 ESTs 1417886 −0.4941304 hypothetical protein FLJ23239 1500815 −0.4934665 Homo sapiens cDNA: FLJ22130 fis, clone HEP19632 868400 −0.4928479 glutaminyl-tRNA synthetase 809894 −0.491862 acetyl-CoA synthetase 753745 −0.4917192 ESTs, Weakly similar to S57447 HPBRII-7 protein [H. sapiens] 85394 −0.4913773 phosphatidic acid phosphatase type 2B 134192 −0.4908497 ESTs 813698 −0.4898644 sprouty (Drosophila) homolog 2 253884 −0.4897811 Human BAC clone GS1-99H8 131012 −0.4897744 hypothetical protein FLJ10633 855755 −0.4897236 fibrillarin 1711456 −0.4896574 H factor (complement)-like 1 815142 −0.4881454 spastic ataxia of Charlevoix-Saguenay (sacsin) 2413337 −0.4879268 sortilin-related receptor, L(DLR class) A repeats-containing 327432 −0.4870045 semaphorin Y 1897944 −0.4855156 ESTs, Weakly similar to T00366 hypothetical protein KIAA0669 [H. sapiens]

Example VI Genes for Discriminating Between Normal and ADH (Non-Malignant) Versus DCIS and IDC (Malignant)

As shown in Table 5 below, 400 genes were identified as being able to discriminate between normal and ADH (non-malignant) versus DCIS and IDC (malignant). TABLE 5 CloneID Weight Description 796469 1.4207633 HSPC150 protein similar to ubiquitin-conjugating enzyme 488964 1.3447179 H2A histone family, member O 1505038 1.3277637 hypothetical protein FLJ20171 1500000 1.2926116 H2B histone family, member B 1554549 1.2787033 hydroxyacyl glutathione hydrolase 812238 1.2664748 hypothetical protein MGC4692 35147 1.2581066 ESTs, Weakly similar to unnamed protein product [H. sapiens] 122077 1.2576139 putative membrane protein 788654 1.2573483 growth factor receptor-bound protein 2 595037 1.2486446 retinoic acid induced 3 565319 1.2155833 Homo sapiens mRNA; cDNA DKFZp564B1264 (from clone DKFZp564B1264) 283919 1.2112507 H2A histone family, member L 1917941 1.1872008 purine-rich element binding protein B 359887 1.1837896 translocase of inner mitochondrial membrane 17 (yeast) homolog A 471568 1.1673113 hematological and neurological expressed 1 290841 1.1670252 H2B histone family, member A 796694 1.1580364 baculoviral IAP repeat-containing 5 (survivin) 366132 1.1440486 succinate dehydrogenase complex, subunit C, integral membrane protein, 15 kD 823598 1.1425746 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 1323448 1.1309009 cysteine-rich protein 1 (intestinal) 810711 1.1074523 stearoyl-CoA desaturase (delta-9-desaturase) 741474 1.0870449 glucose phosphate isomerase 745606 1.0663136 hypothetical protein PP591 2054635 1.0613961 proteasome (prosome, macropain) subunit, alpha type, 7 178805 1.0513873 Human DNA sequence from clone RP5-850E9 on chromosome 20. Contains part of the gene for a novel C2H2 type zinc finger protein similar to Drosophila Scratch (Scrt), Slug and Xenopus Snail, a novel gene similar to Drosophila CG6762, STSs, GSSs and five CpG 347373 1.0454939 transcription elongation factor B (SIII), polypeptide 1 (15 kD, elongin C) 199403 1.0142329 lectin, galactoside-binding, soluble, 8 (galectin 8) 814054 1.0130821 KIAA0040 gene product 2029173 1.0094499 ESTs, Weakly similar to N-WASP [H. sapiens] 209066 1.0066096 782428 1.0008279 KIAA0250 gene product 769921 0.9944462 ubiquitin carrier protein E2-C 470061 0.9920108 seven in absentia (Drosophila) homolog 2 796723 0.9915885 Homo sapiens clone CDABP0014 mRNA sequence 1609836 0.9886168 glutamate-ammonia ligase (glutamine synthase) 2322367 0.9859632 reticulon 4 280375 0.9793036 PRO2000 protein 2016908 0.969649 ESTs, Weakly similar to CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR [H. sapiens] 1858892 0.9669022 hypothetical protein MGC4825 46248 0.9628117 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 2014034 0.9619198 methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase 898032 0.9547022 KIAA0097 gene product 725454 0.9476507 CDC28 protein kinase 2 79520 0.9457391 RAB2, member RAS oncogene family 810558 0.943041 proteasome (prosome, macropain) 26S subunit, ATPase, 4 272529 0.9423688 phosphomannomutase 2 122241 0.939204 proteasome (prosome, macropain) subunit, beta type, 2 469686 0.9381847 Ric (Drosophila)-like, expressed in many tissues 624667 0.9336899 CGI-92 protein 488202 0.932881 ESTs, Weakly similar to YZ28_HUMAN HYPOTHETICAL PROTEIN ZAP128 [H. sapiens] 825470 0.9274271 topoisomerase (DNA) II alpha (170 kD) 1640821 0.920874 ESTs, Weakly similar to I78885 serine/threonine- specific protein kinase [H. sapiens] 686552 0.9182272 golgi phosphoprotein 1 2016648 0.917373 Homo sapiens mRNA; cDNA DKFZp434N1728 (from clone DKFZp434N1728) 1911343 0.9110591 RAB26, member RAS oncogene family 781097 0.9100493 reticulon 3 244801 0.908481 Rho guanine exchange factor (GEF) 11 754628 0.9061145 ESTs 1574058 0.9058211 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) 753299 0.9019921 hypothetical protein FLJ10504 811774 0.9014801 CGI-49 protein 595213 0.8978322 hypothetical protein 868128 0.8970146 JM4 protein 810124 0.8891272 platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29 kD) 66406 0.8888639 hypothetical protein DKFZp762E1312 1636092 0.8841788 hypothetical protein FLJ20657 1869201 0.8825788 hypothetical protein MGC2745 625923 0.8821749 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 1492238 0.8804306 HSPC003 protein 731044 0.8716644 glutaredoxin 2 839682 0.8696528 ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13) 951233 0.8614727 proteasome (prosome, macropain) subunit, beta type, 3 843195 0.8606568 phosphoserine phosphatase 288999 0.8593924 small protein effector 1 of Cdc42 51773 0.8588635 hypothetical protein MGC3077 209066 0.8582298 serine/threonine kinase 15 1474955 0.8573467 TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68 kD (RNA-binding protein 56) 2043167 0.8551193 BCL2-associated athanogene 3 742707 0.8515067 ESTs, Weakly similar to MUC2_HUMAN MUCIN 2 PRECURSOR [H. sapiens] 743589 0.8514377 ESTs, Weakly similar to T2D3_HUMAN TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT [H. sapiens] 704414 0.8498631 small nuclear ribonucleoprotein polypeptides B and B1 2309073 0.8484971 frizzled (Drosophila) homolog 5 2052113 0.8477245 hypothetical protein FLJ10903 686172 0.846207 KIAA0008 gene product 150003 0.8447372 hypothetical protein FLJ13187 705064 0.8401441 transforming, acidic coiled-coil containing protein 3 1709791 0.8397779 BAI1-associated protein 1 1469425 0.8391993 SRY (sex determining region Y)-box 22 429799 0.8386406 hypothetical protein FLJ21939 similar to 5- azacytidine induced gene 2 729975 0.8385313 meningioma expressed antigen 5 (hyaluronidase) 1393018 0.8376676 general transcription factor IIIC, polypeptide 1 (alpha subunit, 220 kD) 1492463 0.8360771 selenoprotein X, 1 2028949 0.8358024 hypothetical protein PRO1855 789012 0.8351735 fibulin 2 470124 0.8347241 RAD1 (S. pombe) homolog 1409509 0.8339967 troponin T1, skeletal, slow 1605426 0.8317254 hypothetical protein FLJ13352 44292 0.831599 Homo sapiens mRNA; cDNA DKFZp434C107 (from clone DKFZp434C107) 1435003 0.8311727 tumor suppressing subtransferable candidate 1 503215 0.8286483 pilin-like transcription factor 504308 0.8199799 hypothetical protein FLJ10540 785707 0.8176557 protein regulator of cytokinesis 1 1500162 0.8155519 ESTs 149355 0.8134342 translocating chain-associating membrane protein 1845169 0.8131362 RAB35, member RAS oncogene family 869375 0.808792 isocitrate dehydrogenase 2 (NADP+), mitochondrial 1492426 0.8032542 chromosome 19 open reading frame 3 782513 0.8030042 interferon, alpha-inducible protein (clone IFI-6-16) 813281 0.8016742 WW domain-containing protein 1 814378 0.8015236 serine protease inhibitor, Kunitz type, 2 700792 0.8005506 cyclin-dependent kinase inhibitor 3 (CDK2- associated dual specificity phosphatase) 340558 0.7990715 actin related protein 2/3 complex, subunit 5 (16 kD) 842994 0.7983201 cathepsin Z 138189 0.7953361 Wolfram syndrome 1 (wolframin) 289978 0.7931469 ubiquitin-like 4 2019223 0.7893602 mitochondrial ribosomal protein L17 2110511 0.7863117 artemin 814528 0.7845635 Homo sapiens cDNA: FLJ22139 fis, clone HEP20959 1573251 0.7816689 peroxisomal long-chain acyl-coA thioesterase 773922 0.7799164 KIAA0005 gene product 172517 0.7779159 hippocalcin-like 1 564981 0.7745626 ESTs 1420370 0.7726877 biliverdin reductase B (flavin reductase (NADPH)) 308466 0.771216 GTP-binding protein Sara 199645 0.769591 nicastrin 1422338 0.7690604 ribonucleotide reductase M2 polypeptide 1474424 0.7689082 Homo sapiens cDNA FLJ12758 fis, clone NT2RP2001328 813751 0.7665427 sialyltransferase 4C (beta-galactosidase alpha- 2,3-sialytransferase) 131094 0.7626373 Homo sapiens cDNA: FLJ21587 fis, clone COL06946 842980 0.762412 developmentally regulated GTP-binding protein 1 212542 0.7585053 Homo sapiens cDNA FLJ12900 fis, clone NT2RP2004321 108425 0.7581954 811761 0.7578696 Nijmegen breakage syndrome 1 (nibrin) 241348 0.757138 prenylcysteine lyase 810725 0.7561061 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21 kD 1460110 0.7559869 proteasome (prosome, macropain) subunit, beta type, 5 120749 0.7545697 ESTs, Moderately similar to KIAA1215 protein [H. sapiens] 827171 0.7543905 ESTs 39884 0.7526496 IMP (inosine monophosphate) dehydrogenase 1 124298 0.7507816 microsomal glutathione S-transferase 3 753378 0.7492212 hypothetical protein FLJ22649 similar to signal peptidase SPC22/23 210862 0.7483198 acyl-Coenzyme A oxidase 1, palmitoyl 785766 0.7476331 hypothetical protein 1553306 0.7471557 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 470099 0.7443747 HT002 protein; hypertension-related calcium- regulated gene 83363 0.7435058 protein-L-isoaspartate (D-aspartate) O- methyltransferase 489351 0.7422879 hypothetical protein DKFZp566J2046 810612 0.7419597 S100 calcium-binding protein A11 (calgizzarin) 825585 0.741258 tubulin-specific chaperone e 1456348 0.7401571 N-acetylneuraminic acid phosphate synthase; sialic acid synthase 1473922 0.7399948 actin related protein 2/3 complex, subunit 3 (21 kD) 150314 0.739762 lysophospholipase I 897806 0.7388301 hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) 811585 0.738212 huntingtin (Huntington disease) 685516 0.7378926 putative G protein-coupled receptor 76605 0.7376829 nesca protein 1476053 0.7367106 RAD51 (S. cerevisiae) homolog (E coli RecA homolog) 221295 0.7342275 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein 824879 0.7333071 hypothetical protein MGC11275 768570 0.732628 hypothetical protein FLJ11280 73009 0.731401 ESTs, Weakly similar to A43932 mucin 2 precursor, intestinal [H. sapiens] 564492 0.7301895 mitochondrial carrier homolog 2 2017415 0.7281714 centromere protein A (17 kD) 788654 0.7244749 488505 0.7242619 accessory proteins BAP31/BAP29 824962 0.7238234 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 1616253 0.7231756 breast carcinoma amplified sequence 1 1435862 0.723081 antigen identified by monoclonal antibodies 12E7, F21 and O13 786067 0.7228184 cell division cycle 25B 2050827 0.7211304 proteasome (prosome, macropain) 26S subunit, ATPase, 5 248649 0.7210707 hypothetical protein FLJ13910 51532 0.7195798 ADP-ribosylation factor-like 6 interacting protein 727078 0.7184618 Homo sapiens cDNA: FLJ23602 fis, clone LNG15735 37708 0.7163849 hypothetical protein MGC3101 430235 0.7162503 H2B histone family, member Q 897770 0.715754 292936 0.7154295 hypothetical protein FLJ10468 365738 0.7152855 ESTs 845363 0.714201 non-metastatic cells 1, protein (NM23A) expressed in 809944 0.7139515 KIAA0310 gene product 1631699 0.7115561 valosin-containing protein 813629 0.7102574 YME1 (S. cerevisiae)-like 1 813410 0.7093173 polymerase (RNA) II (DNA directed) polypeptide K (7.0 kD) 826256 0.7092586 transmembrane 7 superfamily member 1 (upregulated in kidney) 124331 0.7081481 cleavage and polyadenylation specific factors 5, 25 kD subunit 770845 0.7068283 hexokinase 1 67765 0.7064266 carboxypeptidase M 207288 0.7058528 insulin induced gene 1 1639531 0.7033264 RAB27A, member RAS oncogene family 731023 0.7032815 WD repeat domain 5 756442 0.7016064 P450 (cytochrome) oxidoreductase 358162 0.6999211 protein predicted by clone 23627 782608 0.698569 mitochondrial ribosomal protein L9 509823 0.6982362 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 345787 0.6981453 highly expressed in cancer, rich in leucine heptad repeats 810402 0.6978141 hypothetical protein 744417 0.6975761 carnitine acetyltransferase 814306 0.6963874 tumor protein D52 41356 0.6961169 protein phosphatase 2, regulatory subunit B (B56), alpha isoform 813419 0.6951349 hydroxyacyl-Coenzyme A dehydrogenase, type II 629944 0.6950339 myosin VB 327506 0.6943362 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 327506 768064 0.6936336 cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1 770992 0.693225 469383 0.6925975 chromosome 8 open reading frame 1 1492780 0.6923749 Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409 41569 0.691145 hypothetical protein FLJ12650 509588 0.6903363 TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20 kD 144880 0.6902434 hypothetical protein from EUROIMAGE 1759349 789376 0.6883473 thioredoxin reductase 1 268946 0.6881593 WD40 protein Ciao1 810156 0.6879064 deoxythymidylate kinase (thymidylate kinase) 84295 0.6876167 interleukin 1 receptor antagonist 246800 0.6867481 hypothetical protein FLJ10803 589232 0.6865999 hypothetical protein FLJ11506 859761 0.6846134 poliovirus receptor-related 2 (herpesvirus entry mediator B) 431505 0.6840493 ESTs, Highly similar to A31026 probable membrane receptor protein [H. sapiens] 109863 0.683291 epithelial membrane protein 2 770355 0.6829507 lanosterol synthase (2,3-oxidosqualene- lanosterol cyclase) 344091 0.6818771 ESTs 813707 0.6814476 regulator of G-protein signalling 16 124781 0.6809199 squalene epoxidase 502774 0.6807524 hypothetical protein FLJ20623 825740 0.6805157 DKFZp434J1813 protein 1536006 0.6805004 ESTs 203003 0.6802818 non-metastatic cells 4, protein expressed in 785616 0.6800658 signal sequence receptor, alpha (translocon- associated protein alpha) 785840 0.6800437 SEC24 (S. cerevisiae) related gene family, member D 256619 0.6797698 hydroxysteroid (17-beta) dehydrogenase 7 2108077 0.6796871 CGI-112 protein 742595 0.6784804 cyclin-dependent kinase 5 1476065 0.6783519 stathmin 1/oncoprotein 18 68636 0.6778817 hypothetical protein MGC2477 564847 0.6770455 ESTs 744047 0.6748419 polo (Drosophila)-like kinase 897813 0.6741253 polyadenylate binding protein-interacting protein 1 823930 0.6738266 actin related protein 2/3 complex, subunit 1A (41 kD) 236034 0.673506 uncoupling protein 2 (mitochondrial, proton carrier) 743977 0.6729967 Homo sapiens mRNA for TL132 293727 0.6728542 hypothetical protein MGC861 590759 0.672734 sterol-C4-methyl oxidase-like 811024 0.6706275 bone marrow stromal cell antigen 2 785795 0.6683919 hypothetical protein FLJ12910 530310 0.6682042 KIAA0143 protein 1734309 0.666164 sperm associated antigen 4 1898619 0.6651268 hypothetical protein MGC15737 358267 0.6648183 EST, Moderately similar to AF119917 63 PRO2831 [H. sapiens] 753400 0.6633015 CGI-204 protein 292770 0.6609782 Homo sapiens, clone IMAGE: 3627860, mRNA, partial cds 884425 0.6608337 chaperonin containing TCP1, subunit 5 (epsilon) 1696757 0.6599512 hypothetical protein KIAA1165 121251 0.6596925 hypothetical protein MGC5576 770785 0.658751 1,2-alpha-mannosidase IC 590774 0.657447 mitogen-activated protein kinase 13 969877 0.6564571 synaptosomal-associated protein, 25 kD 415102 0.6562436 cell division cycle 25C 120271 0.6562017 hypothetical protein MGC4692 713782 0.6552297 a disintegrin and metalloproteinase domain 15 (metargidin) 49351 0.6551453 SEX gene 488642 0.6541915 ESTs, Weakly similar to I38022 hypothetical protein [H. sapiens] 343607 0.6510034 AD-015 protein 2306987 0.6501071 secreted and transmembrane 1 280249 0.64759 Kruppel-like factor 7 (ubiquitous) 752631 0.6473517 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 489594 0.645574 hypothetical protein FLJ11565 773188 0.6448143 nuclear receptor subfamily 1, group D, member 2 2015517 0.6441737 hypothetical protein FLJ22237 343731 0.6424907 491524 0.6424448 mitochondrial ribosomal protein L13 824524 0.6424419 UDP-galactose transporter related 593431 0.6422897 ESTs, Moderately similar to CEGT_HUMAN CERAMIDE GLUCOSYLTRANSFERASE [H. sapiens] 812994 0.6420817 retinoid X receptor, alpha 1631735 0.6404771 Homo sapiens, clone IMAGE: 3604336, mRNA, partial cds 278531 0.6404612 cytochrome c oxidase subunit VIc 2302099 0.6386686 sialidase 3 (membrane sialidase) 454896 0.6384516 DnaJ (Hsp40) homolog, subfamily A, member 2 1456701 0.6383709 B-cell CLL/lymphoma 9 2055807 0.638184 protein kinase domains containing protein similar to phosphoprotein C8FW 1518402 0.6378481 KIAA1361 protein 810762 0.6371461 SNARE protein 124447 0.6363079 KIAA1184 protein 49273 0.635859 solute carrier family 27 (fatty acid transporter), member 4 365060 0.6350631 RAB11A, member RAS oncogene family 1591264 0.6337293 transaldolase 1 41698 0.6327738 progesterone binding protein 810316 0.6323393 very long-chain acyl-CoA synthetase; lipidosin 826363 0.6322533 lysophospholipase II 2011515 0.6319712 DKFZP586B0923 protein 770675 0.6315109 Homo sapiens cDNA: FLJ21323 fis, clone COL02374 1461477 0.6300096 Homo sapiens mRNA; cDNA DKFZp586I0324 (from clone DKFZp586I0324) 366834 0.629867 envoplakin 1601947 0.6297475 cytochrome c oxidase subunit VIIa polypeptide 2 (liver) 510575 0.6295917 hypothetical protein FLJ22087 503851 0.6291771 nuclear receptor co-repressor/HDAC3 complex subunit 810063 0.6286184 growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration) 754653 0.6277098 cadherin, EGF LAG seven-pass G-type receptor 3, flamingo (I Drosophila) homolog 1518890 0.6251884 metallothionein-like 5, testis-specific (tesmin) 784105 0.6244805 ESTs 205049 0.6231646 protein kinase H11; small stress protein-like protein HSP22 325606 0.6225147 hypothetical protein MGC14353 760299 −1.8441097 dickkopf (Xenopus laevis) homolog 3 200814 −1.8295958 membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) 1882697 −1.715818 peanut (Drosophila)-like 2 344720 −1.6567437 glycophorin C (Gerbich blood group) 1161564 −1.5877154 desmuslin 45099 −1.566311 regucalcin (senescence marker protein-30) 75859 −1.5303427 N-myc downstream-regulated gene 2 811920 −1.5255258 interleukin 11 receptor, alpha 1569187 −1.4872982 heparan sulfate (glucosamine) 3-O- sulfotransferase 4 796542 −1.4697418 ets variant gene 5 (ets-related molecule) 767202 −1.4573536 latent transforming growth factor beta binding protein 2 285377 −1.4496786 pellino (Drosophila) homolog 2 300632 −1.449587 hypothetical protein FLJ21044 similar to Rbig1 160192 −1.4231519 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens ] 611532 −1.3689616 troponin I, skeletal, fast 813265 −1.3632094 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 1469377 −1.359583 lipoma HMGIC fusion partner-like 2 810002 −1.3553375 Homo sapiens, clone MGC: 19762 IMAGE: 3636045, mRNA, complete cds 2056139 −1.3506352 LIM domain protein 377275 −1.3392122 ataxia-telangiectasia group D-associated protein 298122 −1.3364021 frizzled (Drosophila) homolog 7 72778 −1.3299927 caspase 7, apoptosis-related cysteine protease 841308 −1.3246996 myosin, light polypeptide kinase 377461 −1.3214357 caveolin 1, caveolae protein, 22 kD 1473274 −1.3200174 myosin regulatory light chain 2, smooth muscle isoform 1554167 −1.3141843 hypothetical protein FLJ14529 131839 −1.3048208 folate receptor 1 (adult) 67741 −1.3014364 PP2135 protein 132857 −1.280579 Homo sapiens mRNA; cDNA DKFZp586N1323 (from clone DKFZp586N1323) 345670 −1.2805684 ESTs, Moderately similar to I59348 CCAAT binding transcription factor CBF subunit C - rat [R. norvegicus] 781014 −1.2659158 suppression of tumorigenicity 5 289760 −1.2610055 ESTs, Highly similar to T00391 hypothetical protein KIAA0612 [H. sapiens] 742685 −1.248683 disabled (Drosophila) homolog 2 (mitogen- responsive phosphoprotein) 52419 −1.2447753 Friedreich ataxia region gene X123 838478 −1.2349342 neurocalcin delta 839736 −1.2337192 crystallin, alpha B 1558675 −1.2313679 SRY (sex determining region Y)-box 10 796181 −1.2276581 growth arrest-specific 6 878836 −1.2200837 secretory granule, neuroendocrine protein 1 (7B2 protein) 130201 −1.2181641 intercellular adhesion molecule 2 1917449 −1.217371 serum amyloid A4, constitutive 22917 −1.2164705 Homo sapiens mRNA; cDNA DKFZp761M0111 (from clone DKFZp761M0111) 1871116 −1.209237 Homo sapiens mRNA; cDNA DKFZp434C1714 (from clone DKFZp434C1714); partial cds 823871 −1.2090693 SPARC-like 1 (mast9, hevin) 811837 −1.2030392 811848 −1.2011809 hypothetical protein 840266 −1.200789 Homo sapiens cDNA: FLJ22667 fis, clone HSI08385 753071 −1.2005994 Homo sapiens cDNA: FLJ22528 fis, clone HRC12825 2106144 −1.1719133 regulated in glioma 2504881 −1.1674204 signal transducer and activator of transcription 5A 811837 −1.157587 eukaryotic translation elongation factor 1 alpha 1 486683 −1.1548164 Homo sapiens mRNA; cDNA DKFZp564J0323 (from clone DKFZp564J0323) 712139 −1.1491129 ADP-ribosylation factor-like 7 196435 −1.1475545 ESTs 877621 −1.1422087 nGAP-like protein 811088 −1.140941 ephrin-B3 322561 −1.1270333 ribosomal protein L31 712401 −1.1218827 phosphoinositide-3-kinase, catalytic, delta polypeptide 788234 −1.1061158 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 140574 −1.103064 small inducible cytokine subfamily D (Cys-X3- Cys), member 1 (fractalkine, neurotactin) 490023 −1.1020527 hypothetical protein MGC2648 1584540 −1.0933558 Homo sapiens mRNA; cDNA DKFZp586M2022 (from clone DKFZp586M2022) 1556433 −1.0887923 GRO3 oncogene 47043 −1.0841886 tensin 303109 −1.0807576 purinergic receptor (family A group 5) 343760 −1.0803279 SH3 domain binding glutamic acid-rich protein like 2 248631 −1.0784377 aminomethyltransferase (glycine cleavage system protein T) 740620 −1.071175 tropomyosin 2 (beta) 529843 −1.0698218 ESTs, Moderately similar to JC5238 galactosylceramide-like protein, GCP [H. sapiens] 990881 −1.0640807 80344 −1.0602825 interleukin 7 receptor 625399 −1.0594452 hypothetical protein similar to beta-transducin family 416676 −1.0568729 pellino (Drosophila) homolog 1 416959 −1.0566462 nuclear factor I/B 307029 −1.0497874 ribosomal protein L26 488404 −1.0484323 Homo sapiens clone TUA8 Cri-du-chat region mRNA 291478 −1.0400846 runt-related transcription factor 3 153760 −1.0340645 EphB1 119290 −1.025797 cortic al thymocyte receptor (X. laevis CTX) like 814443 −1.0250673 hypothetical protein MGC3232 757191 −1.0238476 ESTs 208718 −1.0229324 annexin A1 161456 −1.0220494 serum amyloid A1 1587710 −1.0209983 period (Drosophila) homolog 1 160609 −1.0208819 ESTs 593023 −1.0158099 dystrobrevin, beta 1878409 −1.013872 catechol-O-methyltransferase 781017 −1.0125987 early growth response 2 (Krox-20 (Drosophila) homolog) 753162 −1.0119485 KIAA0603 gene product 897963 −1.0075423 phosphatidic acid phosphatase type 2A 505864 −1.0033263 RalGDS-like gene 323780 −1.0027215 Homo sapiens cDNA FLJ11177 fis, clone PLACE1007402 343695 −1.002495 hypothetical protein FLJ10875 277571 −0.9977509 KIAA1706 protein 869450 −0.9934083 ribosomal protein L11 280907 −0.9932806 Kruppel-type zinc finger protein 290378 −0.9932643 podocalyxin-like 1635062 −0.9905245 DKFZP586A011 protein 270826 −0.9896888 Homo sapiens cDNA FLJ13329 fis, clone OVARC1001795 1257131 −0.9869928 ESTs

Example VII Genes for Discriminating Between ADH and DCIS

As shown in Table 6 below, 350 genes were identified as being able to discriminate between ADH and DCIS. The actual data is shown in FIG. 3. TABLE 6 CloneID Weight Description 1404774 −0.5685596 parathyroid hormone-like hormone 823871 −0.9429443 SPARC-like 1 (mast9, hevin) 1882697 −1.4318896 peanut (Drosophila)-like 2 140071 −0.5708303 frizzled-related protein 160192 −1.1751869 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens] 796542 −1.2625621 ets variant gene 5 (ets-related molecule) 611532 −1.3158379 troponin I, skeletal, fast 1473274 −1.1172693 myosin regulatory light chain 2, smooth muscle isoform 469306 −0.5113377 gastrin-releasing peptide 2306697 −0.4494025 neuromedin B 132857 −1.0084069 Homo sapiens mRNA; cDNA DKFZp586N1323 (from clone DKFZp586N1323) 2504881 −1.000863 signal transducer and activator of transcription 5A 760299 −1.7010462 dickkopf (Xenopus laevis) homolog 3 293819 −0.4051233 oxidoreductase UCPA 130835 0.3209345 Homo sapiens, Similar to clone FLB3816, clone IMAGE: 3454380, mRNA 66532 −0.5773248 endothelin 3 2499829 −0.3619416 zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia) 85840 −0.7754435 nicotinamide N-methyltransferase 859359 −0.4669761 quinone oxidoreductase homolog 200814 −1.4325283 membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) 825287 −0.2783909 tumor necrosis factor (ligand) superfamily, member 11 202577 −0.2283149 histamine N-methyltransferase 2014373 0.0232775 HNK-1 sulfotransferase 153760 −0.9227865 EphB1 377275 −1.3102234 ataxia-telangiectasia group D-associated protein 745490 −0.6329354 hypothetical protein FLJ20607 172783 −0.6088873 hypothetical protein FLJ10390 1558108 0.0044098 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 1587710 −0.8252065 period (Drosophila) homolog 1 141731 −0.4531468 490484 −0.3388325 ESTs 504959 −0.1620065 Homo sapiens mRNA; cDNA DKFZp586G0321 (from clone DKFZp586G0321) 1609746 −0.4792809 vitelliform macular dystrophy (Best disease, bestrophin) 882248 −0.8700731 transgelin 1917449 −1.0894686 serum amyloid A4, constitutive 2119838 −0.3045374 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8 841507 0.0247736 surfactant, pulmonary-associated protein A2 813265 −1.2230435 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 767202 −1.0654145 latent transforming growth factor beta binding protein 2 1156538 0.2252628 potassium inwardly-rectifying channel, subfamily J, member 11 39600 −0.6540275 adenylate kinase 5 1630990 −0.7312981 ribosomal protein L29 41208 −0.865227 bone morphogenetic protein 1 322561 −0.7970805 ribosomal protein L31 951008 −0.2221875 ESTs 841308 −0.9953716 myosin, light polypeptide kinase 119290 −0.8224756 cortic al thymocyte receptor (X. laevis CTX) like 344959 −0.0998837 gene for serine/threonine protein kinase 810331 −0.1389612 quiescin Q6 1161775 −0.7380353 villin 1 625399 −0.9066615 hypothetical protein similar to beta-transducin family 1470657 −0.3557985 deiodinase, iodothyronine, type II 160609 −0.8405669 ESTs 665356 −0.1575968 tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) 1584540 −0.9754693 Homo sapiens mRNA; cDNA DKFZp586M2022 (from clone DKFZp586M2022) 726779 −0.4459955 calponin 1, basic, smooth muscle 296123 −0.2814132 Homo sapiens PRO1851 mRNA, complete cds 190059 −0.634814 guanine nucleotide binding protein (G protein), gamma 7 1471829 −0.7275378 uncharacterized hypothalamus protein HSMNP1 2056139 −1.0673271 LIM domain protein 190753 −0.4423669 ESTs 1968422 −0.5802058 Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1968422 725390 −0.4620278 glutathione S-transferase pi 814826 −0.8443265 ESTs 878836 −1.037352 secretory granule, neuroendocrine protein 1 (7B2 protein) 27769 −0.8298821 ESTs 188388 −0.6824191 integrin, alpha 10 1597813 −0.5406089 hypothetical protein PP1044 1609625 −0.5920312 selectin P ligand 810981 −0.1805871 hypothetical protein FLJ20699 726703 −0.070084 Homo sapiens clone 23736 mRNA sequence 781014 −1.0161379 suppression of tumorigenicity 5 898222 0.1795078 Homo sapiens clone 24418 mRNA sequence 1475738 −0.6753091 ribosomal protein S25 1492144 −0.2356446 butyrophilin, subfamily 3, member A2 1492147 −0.636656 ribosomal protein S4, X-linked 1711456 −0.4896574 H factor (complement)-like 1 1871116 −0.9821709 Homo sapiens mRNA; cDNA DKFZp434C1714 (from clone DKFZp434C1714); partial cds 344720 −1.5196431 glycophorin C (Gerbich blood group) 45099 −1.3515907 regucalcin (senescence marker protein-30) 307029 −0.6500872 ribosomal protein L26 25763 −0.2725443 ankylosis, progressive (mouse) homolog 2502722 −0.3315871 loss of heterozygosity, 11, chromosomal region 2, gene A 1665444 −0.651994 tumor endothelial marker 1 precursor 165837 −0.3443143 translocase of inner mitochondrial membrane 22 (yeast) homolog 502518 −0.4342228 laminin, beta 2 (laminin S) 897963 −0.9775616 phosphatidic acid phosphatase type 2A 120138 0.1570107 J domain containing protein 1 78946 −0.648366 Homo sapiens pyruvate dehydrogenase kinase 4 mRNA, 3′ untranslated region, partial sequence 990881 −0.8335353 859192 −0.2265317 vesicle-associated membrane protein 1 (synaptobrevin 1) 712023 −0.5302372 AT-binding transcription factor 1 855586 −0.3944697 nuclear receptor subfamily 3, group C, member 1 52419 −1.0368509 Friedreich ataxia region gene X123 432072 −0.4193898 nuclear factor of activated T-cells, cytoplasmic, calcineurin- dependent 1 1897947 −0.163146 surfactant, pulmonary-associated protein A2 727229 −0.2668972 mitogen-activated protein kinase kinase kinase 4 810358 −0.5403705 acyl-Coenzyme A dehydrogenase, very long chain 154600 −0.0683999 phospholipase C, delta 1 755855 −0.6298333 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 323780 −0.8879854 Homo sapiens cDNA FLJ11177 fis, clone PLACE1007402 230560 −0.1803944 ESTs 283173 −0.4293696 EBP50-PDZ interactor of 64 kD 265853 −0.3519023 Homo sapiens cDNA FLJ11298 fis, clone PLACE1009794 161456 −0.8215502 serum amyloid A1 184022 −0.7070266 amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65) 1636523 −0.1496249 glutathione S-transferase subunit 13 homolog 795730 −0.2892776 signal transduction protein (SH3 containing) 1631682 −0.5162406 peptidylprolyl isomerase E (cyclophilin E) 811837 −0.848137 854763 −0.0493902 Homo sapiens cDNA FLJ11341 fis, clone PLACE1010786 50562 −0.0943363 chromosome 8 open reading frame 4 46843 −0.1736687 neuronal Shc adaptor homolog 178137 −0.6839022 ribosomal protein L34 1662279 −0.2290724 plakophilin 1 (ectodermal dysplasia/skin fragility syndrome) 1635062 −0.8243024 DKFZP586A011 protein 293916 −0.3671832 FKBP-associated protein 415613 −0.5528761 DHHC1 protein 80344 −0.8243418 interleukin 7 receptor 1602798 −0.4300808 choline kinase-like 1910516 −0.2845842 ESTs 740620 −0.96496 tropomyosin 2 (beta) 277627 −0.5329107 Human SH3 domain-containing protein SH3P18 mRNA, complete cds 854696 0.008949 siah binding protein 1; FBP interacting repressor; pyrimidine tract binding splicing factor; Ro ribonucleoprotein-binding protein 1 45578 −0.1295485 mitogen-activated protein kinase kinase 6 950710 −0.346361 propionyl Coenzyme A carboxylase, alpha polypeptide 768043 −0.4005598 ECSIT 308539 −0.6726187 Homo sapiens cDNA FLJ12777 fis, clone NT2RP2001720 595637 −0.5373697 Homo sapiens mRNA; cDNA DKFZp586N012 (from clone DKFZp586N012) 143661 −0.4713778 netrin 4 248631 −0.9106505 aminomethyltransferase (glycine cleavage system protein T) 826622 0.1339287 KIAA0430 gene product 51981 −0.5554908 ribosomal protein L7a 811848 −1.1350073 hypothetical protein 1533710 −0.5988282 ortholog of mouse integral membrane glycoprotein LIG-1 2017756 −0.2549438 homolog of yeast MOG1 1637296 −0.5105214 ribosomal protein S24 50586 −0.6794282 KIAA1545 protein 877835 −0.5382125 ribosomal protein L35 773319 −0.285447 ribosomal protein S6 kinase, 70 kD, polypeptide 1 2014888 −0.2871529 sushi-repeat protein 767495 −0.0366213 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 774078 −0.6508021 leiomodin 1 (smooth muscle) 868400 −0.4928479 glutaminyl-tRNA synthetase 240620 −0.5065007 vascular Rab-GAP/TBC-containing 1588791 −0.1606643 O-6-methylguanine-DNA methyltransferase 472186 −0.2687871 RAB32, member RAS oncogene family 725143 −0.3410957 hypothetical protein FLJ22418 714472 −0.3677387 KIAA0397 gene product 1854648 0.0089186 hemopexin 855029 0.076972 Ac-like transposable element 197727 −0.3906866 phosphatidylethanolamine N-methyltransferase 1623016 −0.6263561 EST 813841 0.0885625 plasminogen activator, tissue 2783721 −0.6854649 cholinergic receptor, nicotinic, beta polypeptide 1 (muscle) 549933 −0.3547881 interleukin 8 280907 −0.7307519 Kruppel-type zinc finger protein 796181 −0.8888496 growth arrest-specific 6 415233 −0.6506593 ribosomal protein L37a 811920 −1.2690713 interleukin 11 receptor, alpha 415415 −0.646492 EST, Moderately similar to RL1X_HUMAN 60S RIBOSOMAL PROTEIN L18A [H. sapiens] 2018807 −0.2989936 KIAA0468 gene product 154999 −0.3876757 hypothetical protein FLJ21007 68557 0.0637586 fatty acid binding protein 1, liver 647763 −0.1436566 ESTs 1568967 −0.2938468 ESTs 210717 −0.4522432 syndecan 2 (heparan sulfate proteoglycan 1, cell surface- associated, fibroglycan) 1350439 −0.6740833 KIAA0015 gene product 684582 −0.0089016 tryptophanyl tRNA synthetase 2 (mitochondrial) 122394 −0.049399 guanine nucleotide binding protein (G protein), alpha 15 (Gq class) 213136 −0.1139004 BTG family, member 2 625458 −0.2394796 hypothetical protein MGC3234 811162 −0.3821116 fibromodulin 1926246 −0.701769 ESTs, Moderately similar to T46371 hypothetical protein DKFZp434P1018.1 [H. sapiens] 1554167 −1.0818834 hypothetical protein FLJ14529 811088 −1.0851546 ephrin-B3 72778 −1.1752838 caspase 7, apoptosis-related cysteine protease 220293 −0.5078291 Homo sapiens cDNA: FLJ21800 fis, clone HEP00618 1569187 −1.2971252 heparan sulfate (glucosamine) 3-O-sulfotransferase 4 866866 −0.4801351 Ras association (RalGDS/AF-6) domain family 1 81316 −0.6176265 ESTs 1161564 −1.3891189 desmuslin 898044 −0.4691863 metallocarboxypeptidase CPX-1 293001 −0.4472585 hypothetical protein DKFZp434E2318 1570502 −0.3314609 Homo sapiens cDNA FLJ12936 fis, clone NT2RP2005018 839796 −0.6807912 candidate tumor suppressor p33 ING1 homolog 380883 −0.4438655 Homo sapiens cDNA FLJ10158 fis, clone HEMBA1003463 180561 −0.3250633 glutathione S-transferase M4 869450 −0.7659922 ribosomal protein L11 47043 −0.7729643 tensin 810463 −0.0829995 DKFZP566O084 protein 149539 0.4138942 KIAA1700 200354 −0.0613983 thymidine kinase 2, mitochondrial 771173 0.1757755 mitochondrial ribosomal protein S21 270826 −0.9389651 Homo sapiens cDNA FLJ13329 fis, clone OVARC1001795 810017 −0.1076821 plasminogen activator, urokinase receptor 809838 0.0956351 344168 −0.386185 polymerase (DNA directed), lambda 785967 −0.6049171 erythrocyte membrane protein band 4.1-like 2 511831 −0.2912672 hypothetical protein MGC12936 282404 −0.5528532 Homo sapiens mRNA for KIAA1671 protein, partial cds 730036 −0.079736 Mad4 homolog 298231 −0.3550893 gamma-aminobutyric acid (GABA) B receptor, 1 2106144 −1.067765 regulated in glioma 743880 −0.3262292 KIAA0263 gene product 268234 −0.1535073 Dmx-like 1 280776 −0.2922639 acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 212078 −0.1831462 integrin, alpha 1 731308 0.5371204 citrate synthase 774471 −0.1753902 laminin, beta 1 811837 −0.8764231 eukaryotic translation elongation factor 1 alpha 1 714437 0.0258281 sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B 416959 −0.957248 nuclear factor I/B 681992 −0.7691299 Homo sapiens cDNA FLJ13384 fis, clone PLACE1001062, highly similar to Homo sapiens mRNA for lysine- ketoglutarate reductase/saccharopine dehydrogenase 130201 −1.0401997 intercellular adhesion molecule 2 363144 0.1937891 transcription factor AP-2 beta (activating enhancer-binding protein 2 beta) 857874 −0.3703645 transforming growth factor beta-activated kinase-binding protein 1 377461 −1.2798035 caveolin 1, caveolae protein, 22 kD 156363 0.2685238 hypothetical protein FLJ12934 589115 −0.0115547 matrix metalloproteinase 1 (interstitial collagenase) 241489 −0.6212938 adrenergic, beta-2-, receptor, surface 586725 0.0683397 protein phosphatase 2, regulatory subunit B (B56), beta isoform 283124 −0.7933772 ESTs, Moderately similar to LONG-CHAIN FATTY ACID TRANSPORT PROTEIN [M. musculus] 307328 −0.4022704 hypothetical protein FLJ10948 37449 −0.3539978 GAS2-related on chromosome 22 50892 −0.6887497 Homo sapiens, clone MGC: 9913 IMAGE: 3870821, mRNA, complete cds 1897944 −0.4855156 ESTs, Weakly similar to T00366 hypothetical protein KIAA0669 [H. sapiens] 377314 −0.561312 casein kinase 2, alpha prime polypeptide 220851 −0.0351418 crystallin, alpha A 322233 −0.3025167 586803 −0.7423407 placental growth factor, vascular endothelial growth factor- related protein 343695 −0.7706809 hypothetical protein FLJ10875 414999 −0.5002542 ets variant gene 4 (E1A enhancer-binding protein, E1AF) 813823 −0.4463267 lumican 178825 −0.1525189 neurogranin (protein kinase C substrate, RC3) 85582 −0.0716296 target of myb1 (chicken) homolog-like 2 753620 −0.5248489 insulin-like growth factor binding protein 6 1899338 −0.066168 mannosidase, alpha, class 1A, member 2 359250 0.0674486 carbonic anhydrase IV 345034 −1.0600859 small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK) 2164744 −0.2307289 neural cell adhesion molecule 1 613056 −0.3957342 reticulocalbin 1, EF-hand calcium binding domain 1410444 −0.0368027 amphiregulin (schwannoma-derived growth factor) 593023 −0.7516846 dystrobrevin, beta 788511 0.1403148 ribosomal protein S6 kinase, 90 kD, polypeptide 1 455269 0.0223607 1650927 −0.1712163 hypothetical protein DKFZp547E052 782427 −0.2818886 inhibin, beta B (activin AB beta polypeptide) 71727 −0.2796517 T-cell acute lymphocytic leukemia 1 840942 −0.6383764 major histocompatibility complex, class II, DP beta 1 825470 0.5218731 topoisomerase (DNA) II alpha (170 kD) 595213 0.4824381 hypothetical protein 796694 0.6893307 baculoviral IAP repeat-containing 5 (survivin) 810711 0.9128832 stearoyl-CoA desaturase (delta-9-desaturase) 629944 0.5273447 myosin VB 66406 0.5966701 hypothetical protein DKFZp762E1312 785840 0.5401209 SEC24 (S. cerevisiae) related gene family, member D 210862 0.4683996 acyl-Coenzyme A oxidase 1, palmitoyl 84295 0.3989864 interleukin 1 receptor antagonist 429182 0.2952867 dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit 705064 0.4497555 transforming, acidic coiled-coil containing protein 3 782513 0.4759571 interferon, alpha-inducible protein (clone IFI-6-16) 839682 0.5208954 ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13) 768377 0.3809674 activity-dependent neuroprotective protein 2309073 0.5226599 frizzled (Drosophila) homolog 5 789376 0.4339171 thioredoxin reductase 1 196992 −0.1015205 aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase) 785707 0.4708376 protein regulator of cytokinesis 1 1505038 1.1904802 hypothetical protein FLJ20171 869375 0.4827093 isocitrate dehydrogenase 2 (NADP+), mitochondrial 109221 0.3048287 KIAA0286 protein 345787 0.4647372 highly expressed in cancer, rich in leucine heptad repeats 46248 0.640944 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 79520 0.6769129 RAB2, member RAS oncogene family 469383 0.5558732 chromosome 8 open reading frame 1 509588 0.4157059 TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20 kD 292936 0.4217115 hypothetical protein FLJ10468 686172 0.6724684 KIAA0008 gene product 788655 0.2976191 HTPAP protein 770992 0.3331315 1587847 0.1732392 minichromosome maintenance deficient (mis5, S. pombe) 6 79710 0.4579008 KIAA0174 gene product 2056566 0.2341905 integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide) 454339 0.3738929 thiopurine S-methyltransferase 594226 0.403676 Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409 897813 0.4749348 polyadenylate binding protein-interacting protein 1 824694 0.0268936 protein tyrosine phosphatase type IVA, member 1 725454 0.6669973 CDC28 protein kinase 2 79254 0.0732432 MHC class I region ORF 1472719 0.2550065 SMT3 (suppressor of mif two 3, yeast) homolog 1 2054635 0.7914755 proteasome (prosome, macropain) subunit, alpha type, 7 289978 0.6308861 ubiquitin-like 4 155806 0.2747101 2′-5′-oligoadenylate synthetase 2 (69-71 kD) 147834 0.4412795 zinc finger protein 217 26171 0.3656147 KIAA0856 protein 2322367 0.5832711 reticulon 4 769921 0.6464245 ubiquitin carrier protein E2-C 73009 0.4822587 ESTs, Weakly similar to A43932 mucin 2 precursor, intestinal [H. sapiens] 2014034 0.6620303 methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase 359887 0.8692353 translocase of inner mitochondrial membrane 17 (yeast) homolog A 488964 0.9569176 H2A histone family, member O 1476065 0.289904 stathmin 1/oncoprotein 18 1422338 0.5874097 ribonucleotide reductase M2 polypeptide 268946 0.5440003 WD40 protein Ciao1 686552 0.7231319 golgi phosphoprotein 1 149544 0.283642 neuroepithelial cell transforming gene 1 770675 0.454729 Homo sapiens cDNA: FLJ21323 fis, clone COL02374 346257 0.1515899 minichromosome maintenance deficient (S. cerevisiae) 4 429799 0.6915155 hypothetical protein FLJ21939 similar to 5-azacytidine induced gene 2 143997 0.1883447 proteasome (prosome, macropain) 26S subunit, non- ATPase, 10 122241 0.7394284 proteasome (prosome, macropain) subunit, beta type, 2 823598 0.9153521 proteasome (prosome, macropain) 26S subunit, non- ATPase, 12 814632 0.0960611 splicing factor, arginine/serine-rich (transformer 2 Drosophila homolog) 10 810316 0.3732635 very long-chain acyl-CoA synthetase; lipidosin 290841 0.8346933 H2B histone family, member A 347373 0.7563599 transcription elongation factor B (SIII), polypeptide 1 (15 kD, elongin C) 700792 0.4949149 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 1554549 0.9764206 hydroxyacyl glutathione hydrolase 897770 0.4270685 504308 0.5564295 hypothetical protein FLJ10540 132828 0.2875519 Down syndrome critical region gene 1-like 2 292388 0.112577 1616253 0.567837 breast carcinoma amplified sequence 1 796469 1.0269115 HSPC150 protein similar to ubiquitin-conjugating enzyme 2139152 −0.4373776 Homo sapiens clone 24473 mRNA sequence 130276 0.2154295 Homo sapiens mRNA; cDNA DKFZp586H0324 (from clone DKFZp586H0324) 34149 0.309569 KIAA0227 protein 150003 0.8251408 hypothetical protein FLJ13187 287749 0.3173706 CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1 25380 0.164077 ESTs, Moderately similar to JC5238 galactosylceramide-like protein, GCP [H. sapiens] 745083 0.4107735 ubiquitin specific protease 18 810899 0.240336 CD028 protein kinase 1 768059 0.3139886 hypothetical protein FLJ12619 815026 0.4472842 cleavage stimulation factor, 3′ pre-RNA, subunit 3, 77 kD 741474 0.7732047 glucose phosphate isomerase 788641 0.3638059 adaptor-related protein complex 1, sigma 2 subunit 2043167 0.7167431 BCL2-associated athanogene 3 1492780 0.6544659 Homo sapiens cDNA FLJ14459 fis, clone HEMBB1002409 2306987 0.4402912 secreted and transmembrane 1 754653 0.4405873 cadherin, EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog 743810 0.3667087 hypothetical protein MGC2577 126858 0.2389814 sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1 2017415 0.43546 centromere protein A (17 kD) 280507 0.2846518 hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome) 67237 0.1406869 ESTs 43833 −0.1197546 diacylglycerol kinase, gamma (90 kD) 42076 0.3194462 TRK-fused gene 531319 0.1093932 serine/threonine kinase 12 784129 0.2902598 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide 586895 0.2549108 small nuclear ribonucleoprotein polypeptide G

Example VIII Genes for Discriminating Between DCIS Grade I and Grade III

As shown in Table 7 below, 350 genes were identified as being able to discriminate between grades of DCIS. The actual data corresponding to this table is shown in FIG. 4. TABLE 7 CloneID Weight Description 2460159 4.6268975 tyrosine kinase, non-receptor, 1 358151 2.8783989 zinc finger protein 33a (KOX 31) 795382 2.772572 Rap1 guanine-nucleotide-exchange factor directly activated by cAMP 714472 2.6829714 KIAA0397 gene product 725649 2.6433625 nuclear factor of activated T-cells, cytoplasmic, calcineurin- dependent 4 51218 2.6200167 ESTs 504959 2.5777963 Homo sapiens mRNA; cDNA DKFZp586G0321 (from clone DKFZp586G0321) 647397 2.5320153 ESTs 814815 2.4198892 plakophilin 4 279720 2.4136316 ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens] 298231 2.4096172 gamma-aminobutyric acid (GABA) B receptor, 1 172783 2.3339699 hypothetical protein FLJ10390 261609 2.311051 ESTs, Weakly similar to S65657 alpha-1C-adrenergic receptor splice form 2 [H. sapiens] 826668 2.2951137 KIAA0274 gene product 1493383 2.2616737 Homo sapiens mRNA; cDNA DKFZp434H2418 (from clone DKFZp434H2418) 2017756 2.2403622 homolog of yeast MOG1 1455566 2.1756946 adenosine A3 receptor 725321 2.1658095 estrogen receptor 1 180561 2.1393944 glutathione S-transferase M4 32050 2.1165022 Homo sapiens mRNA; cDNA DKFZp586P1124 (from clone DKFZp586P1124) 215000 2.1150123 vasoactive intestinal peptide receptor 1 2019750 2.0957741 SEC14 (S. cerevisiae)-like 2 283124 2.0921779 ESTs, Moderately similar to LONG-CHAIN FATTY ACID TRANSPORT PROTEIN [M. musculus] 490615 2.0635424 tubulin, gamma 2 666138 2.0625667 hypothetical protein DKFZp761J1523 418129 2.0541212 nuclear mitotic apparatus protein 1 1733262 2.052666 BLu protein 1588791 2.044069 O-6-methylguanine-DNA methyltransferase 461761 2.035953 angiogenin, ribonuclease, RNase A family, 5 1031592 1.9930012 kinesin protein 9 gene 126415 1.9781057 Homo sapiens mRNA; cDNA DKFZp566H0124 (from clone DKFZp566H0124) 28643 1.9733043 hypothetical protein DKFZp564D1378 470261 1.9160486 1630990 1.9155421 ribosomal protein L29 810981 1.9132205 hypothetical protein FLJ20699 767495 1.9052671 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 767176 1.8996792 tumor necrosis factor (ligand) superfamily, member 13 1572196 1.8855996 secreted modular calcium-binding protein 2 1706635 1.8754346 bone gamma-carboxyglutamate (gla) protein (osteocalcin) 186301 1.8424458 Homo sapiens cDNA FLJ12924 fis, clone NT2RP2004709 726703 1.842399 Homo sapiens clone 23736 mRNA sequence 214205 1.8416657 Homo sapiens, clone MGC: 17687 IMAGE: 3865868, mRNA, complete cds 784178 1.822159 Homo sapiens mRNA; cDNA DKFZp586M0723 (from clone DKFZp586M0723) 346902 1.8196723 ESTs, Weakly similar to ALU2_HUMAN ALU SUBFAMILY SB SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 1367678 1.8184255 KIAA0356 gene product 190059 1.7988757 guanine nucleotide binding protein (G protein), gamma 7 1456937 1.7980645 oviductal glycoprotein 1, 120 kD (mucin 9, oviductin) 45578 1.7935215 mitogen-activated protein kinase kinase 6 248631 1.7701919 aminomethyltransferase (glycine cleavage system protein T) 1562231 1.7668811 SET binding protein 1 154466 1.7516237 STIP1 homology and U-Box containing protein 1 2524445 1.7392197 neuronal PAS domain protein 1 277266 1.7307752 Homo sapiens, clone IMAGE: 3625550, mRNA, partial cds 741891 1.7297992 RAB2, member RAS oncogene family-like 206217 1.7227658 nuclear receptor subfamily 1, group H, member 3 2028876 1.7128178 splicing factor, arginine/serine-rich 5 730036 1.70573 Mad4 homolog 1558233 1.7035129 ESTs 502518 1.7027287 laminin, beta 2 (laminin S) 356835 1.7014349 hypothetical protein MGC10500 744994 1.6938348 hypothetical protein FLJ12242 810358 1.6924263 acyl-Coenzyme A dehydrogenase, very long chain 813854 1.6914133 purine-rich element binding protein A 768043 1.6854123 ECSIT 264632 1.6591646 ESTs 505243 1.6581518 inositol 1,4,5-triphosphate receptor, type 2 344073 1.6571604 ESTs, Weakly similar to K1CI_HUMAN KERATIN, TYPE I CYTOSKELETAL 9 [H. sapiens] 343760 1.6435915 SH3 domain binding glutamic acid-rich protein like 2 1569418 1.6408767 Homo sapiens cDNA FLJ11385 fis, clone HEMBA1000520 202577 1.6393518 histamine N-methyltransferase 823634 1.6366047 ESTs 839796 1.630887 candidate tumor suppressor p33 ING1 homolog 183440 1.6297915 arylsulfatase A 344959 1.6268043 gene for serine/threonine protein kinase 1574252 1.6211224 DKFZP586D0623 protein 669359 1.6174855 Homo sapiens clone 24405 mRNA sequence 74070 1.6096611 endosulfine alpha 1660649 1.6051582 suppressor of white apricot homolog 2 796723 1.6041219 Homo sapiens clone CDABP0014 mRNA sequence 743146 1.597094 hypothetical protein FLJ23403 789147 1.5937127 enolase 2, (gamma, neuronal) 342181 1.5926355 B-cell CLL/lymphoma 2 33076 1.5824352 cholinephosphotransferase 1 782497 1.5804781 Homo sapiens, clone IMAGE: 3010666, mRNA, partial cds 470261 1.5751564 SMA5 809507 1.5723669 hypothetical protein FLJ20568 712460 1.5721924 natural killer-tumor recognition sequence 293569 1.5662317 chromosome 1 open reading frame 21 1518402 1.5627158 KIAA1361 protein 155072 1.5557559 ESTs 455269 1.5538593 262804 1.5532348 hypothetical protein MGC2941 1492238 1.5484044 HSPC003 protein 364865 1.5483958 hypothetical protein FLJ21062 2325804 1.5461823 95 kDa retinoblastoma protein binding protein 1635062 1.5449944 DKFZP586A011 protein 344168 1.5421405 polymerase (DNA directed), lambda 1517171 1.5381921 interleukin 2 receptor, alpha 769600 1.5335878 uracil-DNA glycosylase 2 325583 1.5245817 EST 814826 1.5223296 ESTs 1570502 1.5184543 Homo sapiens cDNA FLJ12936 fis, clone NT2RP2005018 511831 1.5183298 hypothetical protein MGC12936 124922 1.5052004 KRAB-zinc finger protein SZF1-1 2072768 1.4886791 nuclear receptor coactivator 3 2021882 1.4854251 sodium channel, nonvoltage-gated 1, delta 627248 1.4827018 SBBI31 protein 725503 1.476461 D-dopachrome tautomerase 285312 1.4699425 141731 1.469088 1456701 1.4668054 B-cell CLL/lymphoma 9 898222 1.4667947 Homo sapiens clone 24418 mRNA sequence 725284 1.4638006 phosphorylase kinase, gamma 2 (testis) 154999 1.4564204 hypothetical protein FLJ21007 1592530 1.4558873 mammalian inositol hexakisphosphate kinase 2 590310 1.4534138 Homo sapiens mRNA; cDNA DKFZp434E2321 (from clone DKFZp434E2321); partial cds 416042 1.446691 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 2017144 1.4450059 CGI-41 protein 309449 1.4412699 ribosomal protein S4, Y-linked 450301 1.4403678 mutL (E. coli) homolog 3 1492468 1.4375076 DEME-6 protein 121454 1.4361788 arachidonate 12-lipoxygenase 743880 1.4294838 KIAA0263 gene product 1568967 1.4109448 ESTs 1568989 1.4094472 ESTs 25274 1.4078252 g20 protein 2413337 1.4058288 sortilin-related receptor, L(DLR class) A repeats-containing 197913 1.3994468 splicing factor proline/glutamine rich (polypyrimidine tract- binding protein-associated) 292770 1.3952057 Homo sapiens, clone IMAGE: 3627860, mRNA, partial cds 143332 1.3875805 neuropeptide Y receptor Y1 809779 1.3848708 KIAA0239 protein 138242 1.3820433 ESTs, Moderately similar to MAS2_HUMAN MANNAN- BINDING LECTIN SERINE PROTEASE 2 PRECURSOR [H. sapiens] 270127 1.3786197 49240 1.3772023 KIAA0460 protein 826622 1.3734143 KIAA0430 gene product 1858837 1.3719341 ESTs 1583198 1.3712112 ESTs, Weakly similar to S65824 reverse transcriptase homolog [H. sapiens] 345858 1.3629187 cisplatin resistance associated 208387 1.3597205 KIAA1407 protein 502782 1.3589088 RAN binding protein 3 26294 1.3578289 RNB6 669379 1.3559931 Homo sapiens BAC clone RP11-505D17 from 7p22-p21 810728 1.355262 hypothetical gene ZD52F10 1601845 1.3533864 Ca2+-promoted Ras inactivator 840882 1.350538 nucleotide binding protein 82173 1.3485351 MYLE protein 490965 1.3476943 ESTs 811162 1.3450626 fibromodulin 61061 1.3437368 hypothetical protein FLJ20585 49630 1.3412751 calcium channel, voltage-dependent, L type, alpha 1D subunit 825659 −2.8345933 N-myc downstream regulated 769921 −2.712812 ubiquitin carrier protein E2-C 788232 −2.6550962 sestrin 2 1476053 −2.529039 RAD51 (S. cerevisiae) homolog (E coli RecA homolog) 809557 −2.4910488 minichromosome maintenance deficient (S. cerevisiae) 3 150897 −2.4302462 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 3 814526 −2.37273 seb4D 796694 −2.3104815 baculoviral IAP repeat-containing 5 (survivin) 814792 −2.3001334 ubiquitin specific protease 10 1536236 −2.2971152 hypothetical protein FLJ13154 2017415 −2.2748559 centromere protein A (17 kD) 210862 −2.2408114 acyl-Coenzyme A oxidase 1, palmitoyl 795543 −2.2403389 thioredoxin peroxidase (antioxidant enzyme) 773301 −2.2239527 cadherin 3, type 1, P-cadherin (placental) 700792 −2.2203557 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 1883327 −2.2093248 ESTs 1523225 −2.1936598 oncostatin M receptor 208718 −2.1882654 annexin A1 1702742 −2.1567809 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 753378 −2.151145 hypothetical protein FLJ22649 similar to signal peptidase SPC22/23 429222 −2.1351022 CGI-107 protein 292388 −2.1343367 781047 −2.1262682 budding uninhibited by benzimidazoles 1 (yeast homolog) 450854 −2.0819596 craniofacial development protein 1 823598 −2.0693353 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 1422338 −2.0689327 ribonucleotide reductase M2 polypeptide 705064 −2.0601901 transforming, acidic coiled-coil containing protein 3 770675 −2.0272207 Homo sapiens cDNA: FLJ21323 fis, clone COL02374 345787 −1.9992897 highly expressed in cancer, rich in leucine heptad repeats 471196 −1.9985751 integral membrane protein 3 753215 −1.9954476 guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 869375 −1.9803724 isocitrate dehydrogenase 2 (NADP+), mitochondrial 842818 −1.9796507 lysyl-tRNA synthetase 229579 −1.9782493 Golgi apparatus protein 1 1916461 −1.9736332 hypothetical protein 129294 −1.9730334 ESTs 789376 −1.9719575 thioredoxin reductase 1 1897302 −1.9681938 serine/threonine kinase 17b (apoptosis-inducing) 951117 −1.9577807 eukaryotic translation elongation factor 1 gamma 1642496 −1.9484342 hypothetical protein MGC11266 591465 −1.9277062 Homo sapiens, clone MGC: 2908 IMAGE: 3029644, mRNA, complete cds 149355 −1.8999907 translocating chain-associating membrane protein 259950 −1.8958779 hypothetical protein FLJ14991 897770 −1.8887034 878798 −1.8774101 beta-2-microglobulin 746229 −1.873434 mitogen-activated protein kinase kinase kinase kinase 4 624867 −1.8594915 hypothetical protein FLJ20186 504308 −1.8590049 hypothetical protein FLJ10540 727251 −1.8553757 CD9 antigen (p24) 897774 −1.8532125 adenine phosphoribosyltransferase 1901310 −1.8434048 KIAA1209 protein 292936 −1.838542 hypothetical protein FLJ10468 1518591 −1.8382765 321354 −1.8123042 mitochondrial ribosomal protein L15 1903066 −1.8071117 keratin, hair, basic, 1 235180 −1.8004039 ESTs, Moderately similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 740604 −1.7995578 interferon stimulated gene (20 kD) 233464 −1.7978669 epithelial V-like antigen 1 951241 −1.7961406 clone HQ0310 PRO0310p1 1587847 −1.7886092 minichromosome maintenance deficient (mis5, S. pombe) 6 624390 −1.7800152 DC13 protein 128711 −1.7791673 anillin (Drosophila Scraps homolog), actin binding protein 308633 −1.7667341 hypothetical protein FLJ10339 884425 −1.761486 chaperonin containing TCP1, subunit 5 (epsilon) 745394 −1.7583344 Homo sapiens cDNA: FLJ23249 fis, clone COL04196 852829 −1.7579704 karyopherin alpha 3 (importin alpha 4) 122241 −1.7490794 proteasome (prosome, macropain) subunit, beta type, 2 307255 −1.7294781 basement membrane-induced gene 32493 −1.7273675 integrin, alpha 6 454896 −1.7216328 DnaJ (Hsp40) homolog, subfamily A, member 2 1876217 −1.7186822 DnaJ (Hsp40) homolog, subfamily A, member 2 815556 −1.7161709 hypothetical protein FLJ10430 589869 −1.7120206 transcriptional co-activator with PDZ-binding motif (TAZ) 2012523 −1.7104314 fatty acid binding protein 5 (psoriasis-associated) 1946448 −1.7092537 caveolin 2 841370 −1.7047297 glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) 1600239 −1.6989076 HSPC037 protein 462926 −1.6981004 NIMA (never in mitosis gene a)-related kinase 2 144880 −1.6980733 hypothetical protein from EUROIMAGE 1759349 744047 −1.6910803 polo (Drosophila)-like kinase 624627 −1.6888444 ribonucleotide reductase M2 polypeptide 788566 −1.6752673 Purkinje cell protein 4 858293 −1.6732706 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide 470148 −1.659943 ESTs 66902 −1.6546363 ESTs 77533 −1.6505418 inositol polyphosphate-5-phosphatase, 40 kD 825282 −1.6417354 DKFZP586L0724 protein 785840 −1.6406565 SEC24 (S. cerevisiae) related gene family, member D 824962 −1.6399941 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 741139 −1.6396499 eyes absent (Drosophila) homolog 2 809530 −1.6264151 minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin) 2054635 −1.6254343 proteasome (prosome, macropain) subunit, alpha type, 7 813533 −1.6215197 syndecan binding protein (syntenin) 267816 −1.6173276 KIAA0551 protein 306318 −1.6083862 origin recognition complex, subunit 6 (yeast homolog)-like 796469 −1.6065509 HSPC150 protein similar to ubiquitin-conjugating enzyme 813256 −1.6027042 ATP-binding cassette, sub-family B (MDR/TAP), member 1 843121 −1.60128 chloride intracellular channel 1 713685 −1.6006729 protease, serine, 2 (trypsin 2) 811590 −1.6001102 hypothetical protein FLJ11100 823756 −1.5995448 mitogen inducible 2 549073 −1.597146 capping protein (actin filament) muscle Z-line, alpha 2 743810 −1.5960999 hypothetical protein MGC2577 377368 −1.5955102 cell death regulator aven 1506046 −1.5918448 hypothetical protein FLJ10815 814270 −1.5890389 polymyositis/scleroderma autoantigen 1 (75 kD) 1604703 −1.5853167 major histocompatibility complex, class I, F 234736 −1.5765159 GATA-binding protein 6 429182 −1.5699689 dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit 826355 −1.5677013 vesicle-associated membrane protein 5 (myobrevin) 34149 −1.5659923 KIAA0227 protein 746190 −1.5635857 hypothetical protein DKFZp761B1514 131091 −1.558448 Not56 (D. melanogaster)-like protein 665384 −1.5550415 KIAA1609 protein 625683 −1.5501423 neighbor of COX4 1582738 −1.544427 uncharacterized bone marrow protein BM040 949988 −1.5437326 Homo sapiens mRNA; cDNA DKFZp586E1124 (from clone DKFZp586E1124); complete cds 133213 −1.5433392 fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid- specific) 1660666 −1.5423907 carbonic anhydrase VB, mitochondrial 713158 −1.5372729 ESTs 1614140 −1.5341302 Ris 201890 −1.5333626 baculoviral IAP repeat-containing 3 38925 −1.5304604 ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens] 511850 −1.5294752 proteasome (prosome, macropain) 26S subunit, ATPase, 1 489489 −1.5169076 lamin B receptor 825470 −1.5154306 topoisomerase (DNA) II alpha (170 kD) 42831 −1.5136459 N-terminal kinase-like 809784 −1.5066053 kallikrein 6 (neurosin, zyme) 730410 −1.506168 lymphocyte-specific protein tyrosine kinase 810983 −1.5060386 DKFZP434H132 protein 731223 −1.5058799 proteasome (prosome, macropain) subunit, beta type, 2 259017 −1.5053827 ESTs 340745 −1.5041978 ESTs 746163 −1.5000358 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 1466621 −1.4998321 ATPase, Ca++ transporting, type 2C, member 1 809588 −1.49754 gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) 813707 −1.4946872 regulator of G-protein signalling 16 188335 −1.4895328 egf-like module containing, mucin-like, hormone receptor-like sequence 2 1493160 −1.4851884 small inducible cytokine subfamily B (Cys-X-Cys), member 10 531886 −1.4842053 Homo sapiens clone FLB3344 PRO0845 mRNA, complete cds 753428 −1.4835152 Homo sapiens, clone IMAGE: 3542597, mRNA, partial cds 897731 −1.4833877 latrophilin 376551 −1.4811859 ETAA16 protein 256907 −1.4755682 glutathione S-transferase A3 712139 −1.4735772 ADP-ribosylation factor-like 7 785368 −1.4680554 PDZ-binding kinase; T-cell originated protein kinase 825606 −1.4667088 kinesin-like 1 531319 −1.4659871 serine/threonine kinase 12 66406 −1.4641179 hypothetical protein DKFZp762E1312 470124 −1.4635711 RAD1 (S. pombe) homolog

Example IX Genes for Discriminating Between IDC Grade I and Grade III

As shown in Table 8 below, 300 genes were identified as being able to discriminate between two grades of IDC. TABLE 8 CloneID Weight Description 1706635 3.279305 bone gamma-carboxyglutamate (gla) protein (osteocalcin) 666138 3.1366533 hypothetical protein DKFZp761J1523 795382 3.0005724 Rap1 guanine-nucleotide-exchange factor directly activated by cAMP 364865 2.8512705 hypothetical protein FLJ21062 1500542 2.8021264 regulator of G-protein signalling 11 270127 2.7455118 588262 2.7127609 Homo sapiens, Similar to RIKEN cDNA 2600001A11 gene, clone MGC: 9907 IMAGE: 3870073, mRNA, complete cds 277266 2.5004627 Homo sapiens, clone IMAGE: 3625550, mRNA, partial cds 2090129 2.4882736 chromobox homolog 2 (Drosophila Pc class) 325583 2.4558352 EST 358151 2.4309122 zinc finger protein 33a (KOX 31) 786675 2.3877233 epididymis-specific, whey-acidic protein type, four-disulfide core; putative ovarian carcinoma marker 854763 2.378956 Homo sapiens cDNA FLJ11341 fis, clone PLACE1010786 1592976 2.3417116 microphthalmia-associated transcription factor 1562231 2.286418 SET binding protein 1 767176 2.2472282 tumor necrosis factor (ligand) superfamily, member 13 784178 2.2026739 Homo sapiens mRNA; cDNA DKFZp586M0723 (from clone DKFZp586M0723) 811162 2.1926501 fibromodulin 502518 2.1886432 laminin, beta 2 (laminin S) 754429 2.1363368 ESTs, Weakly similar to T00084 hypothetical protein KIAA0512 [H. sapiens] 214205 2.1127961 Homo sapiens, clone MGC: 17687 IMAGE: 3865868, mRNA, complete cds 61061 2.1046094 hypothetical protein FLJ20585 344959 2.0756965 gene for serine/threonine protein kinase 814815 2.0694714 plakophilin 4 262804 2.0673444 hypothetical protein MGC2941 1455566 2.0489061 adenosine A3 receptor 1469149 1.9778151 Homo sapiens clone 24606 mRNA sequence 358217 1.9703763 glypican 4 206217 1.9595484 nuclear receptor subfamily 1, group H, member 3 261609 1.958083 ESTs, Weakly similar to S65657 alpha-1C-adrenergic receptor splice form 2 [H. sapiens] 197525 1.9550731 flavin containing monooxygenase 5 857640 1.9532398 collagen, type VI, alpha 2 812143 1.9469226 fibronectin leucine rich transmembrane protein 3 898222 1.9409805 Homo sapiens clone 24418 mRNA sequence 418129 1.9385868 nuclear mitotic apparatus protein 1 2021882 1.9213983 sodium channel, nonvoltage-gated 1, delta 293819 1.919948 oxidoreductase UCPA 203003 1.8989675 non-metastatic cells 4, protein expressed in 705274 1.8986548 diacylglycerol kinase, delta (130 kD) 124922 1.8975916 KRAB-zinc finger protein SZF1-1 2505310 1.8859615 calcium/calmodulin-dependent protein kinase I 1492238 1.8795818 HSPC003 protein 810358 1.8732889 acyl-Coenzyme A dehydrogenase, very long chain 2391494 1.8698169 ephrin-A4 1592530 1.8669954 mammalian inositol hexakisphosphate kinase 2 810671 1.8659671 hypothetical protein FLJ22269 2108048 1.8648249 DNB5 730036 1.8564918 Mad4 homolog 810741 1.831265 GABA(A) receptor-associated protein 45578 1.8274273 mitogen-activated protein kinase kinase 6 647397 1.8263711 ESTs 767495 1.8149096 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 32050 1.8117146 Homo sapiens mRNA; cDNA DKFZp586P1124 (from clone DKFZp586P1124) 811848 1.8106436 hypothetical protein 186301 1.8021505 Homo sapiens cDNA FLJ12924 fis, clone NT2RP2004709 366526 1.7836259 ESTs, Weakly similar to ALU5_HUMAN ALU SUBFAMILY SC SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 813154 1.7815662 nuclear factor I/A 85195 1.778695 growth arrest and DNA-damage-inducible, gamma 2460159 1.7730834 tyrosine kinase, non-receptor, 1 504959 1.7723846 Homo sapiens mRNA; cDNA DKFZp586G0321 (from clone DKFZp586G0321) 742094 1.7684813 hypothetical protein FLJ20950 256619 1.7658619 hydroxysteroid (17-beta) dehydrogenase 7 726699 1.7594888 ESTs, Weakly similar to AAB47496 NG5 [H. sapiens] 2017144 1.7514699 CGI-41 protein 74070 1.7336683 endosulfine alpha 1762111 1.7236006 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 795750 1.7116475 Homo sapiens clone 25056 mRNA sequence 2019750 1.7095011 SEC14 (S. cerevisiae)-like 2 2325804 1.7039903 95 kDa retinoblastoma protein binding protein 279720 1.693594 ESTs, Moderately similar to A47582 B-cell growth factor precursor [H. sapiens] 132857 1.6875688 Homo sapiens mRNA; cDNA DKFZp586N1323 (from clone DKFZp586N1323) 1898619 1.684954 hypothetical protein MGC15737 681992 1.6802347 Homo sapiens cDNA FLJ13384 fis, clone PLACE1001062, highly similar to Homo sapiens mRNA for lysine-ketoglutarate reductase/saccharopine dehydrogenase 85450 1.6753438 acyl-Coenzyme A oxidase 2, branched chain 51218 1.6748931 ESTs 1925280 1.6563658 homologous to yeast nitrogen permease (candidate tumor suppressor) 250883 1.6504115 ubiquitin-activating enzyme E1-like 172783 1.6502064 hypothetical protein FLJ10390 208387 1.6498608 KIAA1407 protein 703964 1.6452497 inositol polyphosphate phosphatase-like 1 298231 1.6428171 gamma-aminobutyric acid (GABA) B receptor, 1 277848 1.6407233 ADP-ribosylation factor 6 669359 1.6386236 Homo sapiens clone 24405 mRNA sequence 321455 1.6327309 Homo sapiens, Similar to RIKEN cDNA 1110002C08 gene, clone MGC: 9564 IMAGE: 3872267, mRNA, complete cds 796152 1.6295159 Homo sapiens cDNA FLJ11685 fis, clone HEMBA1004934 502782 1.614818 RAN binding protein 3 360778 1.6091782 950574 1.606032 H3 histone, family 3B (H3.3B) 788334 1.5816572 mitochondrial ribosomal protein L23 782497 1.5767626 Homo sapiens, clone IMAGE: 3010666, mRNA, partial cds 1733262 1.5656438 BLu protein 342181 1.5642436 B-cell CLL/lymphoma 2 1632248 1.5590794 Homo sapiens cDNA FLJ14181 fis, clone NT2RP2004300 1526826 1.5576997 homeo box B2 145132 1.5520317 mannose-P-dolichol utilization defect 1 183062 1.5400324 ubiquitin specific protease 21 823663 1.5337257 fragile X mental retardation, autosomal homolog 2 190059 1.5258594 guanine nucleotide binding protein (G protein), gamma 7 111721 1.5045285 insulin induced protein 2 840882 1.5039692 nucleotide binding protein 1902764 1.5037016 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 414999 1.5021506 ets variant gene 4 (E1A enhancer-binding protein, E1AF) 1636523 1.4948923 glutathione S-transferase subunit 13 homolog 594683 1.4862053 ESTs 1916575 1.4825298 BCL2-interacting killer (apoptosis-inducing) 1456937 1.4730662 oviductal glycoprotein 1, 120 kD (mucin 9, oviductin) 25274 1.464238 g20 protein 795288 1.4625618 ubiquitin specific protease 4 (proto-oncogene) 1569418 1.4599089 Homo sapiens cDNA FLJ11385 fis, clone HEMBA1000520 753700 1.4522717 Ras-related GTP-binding protein 1691237 1.4516493 ESTs 741891 1.450795 RAB2, member RAS oncogene family-like 1493383 1.4468163 Homo sapiens mRNA; cDNA DKFZp434H2418 (from clone DKFZp434H2418) 1675273 1.445145 RAR-related orphan receptor C 293916 1.4265341 FKBP-associated protein 39600 1.4224626 adenylate kinase 5 1573087 1.4200341 KIAA0592 protein 839796 1.4114662 candidate tumor suppressor p33 ING1 homolog 296123 1.4057088 Homo sapiens PRO1851 mRNA, complete cds 727263 1.4046408 heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) 265045 1.4041143 Homo sapiens mRNA; cDNA DKFZp586B0918 (from clone DKFZp586B0918) 869450 1.4034983 ribosomal protein L11 714472 1.4006155 KIAA0397 gene product 825296 1.3963737 low density lipoprotein receptor defect C complementing 753301 1.3962897 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 700527 1.394937 glutaredoxin (thioltransferase) 811565 1.3909974 KIAA1694 protein 1630990 1.3843882 ribosomal protein L29 70749 1.3810753 Homo sapiens cDNA: FLJ21874 fis, clone HEP02488 814826 1.3785178 ESTs 175103 1.376581 cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog 215000 1.3677098 vasoactive intestinal peptide receptor 1 810331 1.3656069 quiescin Q6 1681421 1.3645145 EGF-like-domain, multiple 3 502198 1.3619124 protein phosphatase 1, regulatory (inhibitor) subunit 5 825365 1.361275 hypothetical protein FLJ21919 1557047 1.3582677 thrombospondin 3 2067500 1.3579293 Z-band alternatively spliced PDZ-motif 490615 1.3566637 tubulin, gamma 2 743880 1.3528093 KIAA0263 gene product 812099 1.3444147 RNA binding motif protein 5 868652 1.3432331 complement component 4B 120138 1.3384804 J domain containing protein 1 156363 1.3358314 hypothetical protein FLJ12934 813584 1.3327194 p53 regulated PA26 nuclear protein 726703 1.3247883 Homo sapiens clone 23736 mRNA sequence 809507 1.3225829 hypothetical protein FLJ20568 2018423 1.3212314 death-associated protein kinase 2 292806 1.3201283 chromosome segregation 1 (yeast homolog)-like 741977 1.3200635 B-factor, properdin 610326 −4.5776738 322494 −3.6341126 core-binding factor, beta subunit 824962 −3.6328144 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 825659 −3.6247426 N-myc downstream regulated 796694 −3.5038212 baculoviral IAP repeat-containing 5 (survivin) 149355 −3.4959791 translocating chain-associating membrane protein 814270 −3.3246381 polymyositis/scleroderma autoantigen 1 (75 kD) 884425 −3.3113482 chaperonin containing TCP1, subunit 5 (epsilon) 1874367 −3.2390912 small inducible cytokine subfamily A (Cys—Cys), member 20 742707 −3.2093502 ESTs, Weakly similar to MUC2_HUMAN MUCIN 2 PRECURSOR [H. sapiens] 321354 −3.1386611 mitochondrial ribosomal protein L15 280375 −3.110486 PRO2000 protein 2018154 −3.0906181 electron-transfer-flavoprotein, beta polypeptide 814792 −3.0561472 ubiquitin specific protease 10 826070 −3.0517117 KIAA0948 protein 624867 −2.9688171 hypothetical protein FLJ20186 202035 −2.9361687 uncharacterized hypothalamus protein HT010 1476053 −2.9129535 RAD51 (S. cerevisiae) homolog (E coli RecA homolog) 194318 −2.8913426 hypothetical protein MGC5585 769921 −2.8415969 ubiquitin carrier protein E2-C 1732922 −2.8216808 Homo sapiens mRNA; cDNA DKFZp762H106 (from clone DKFZp762H106) 1536236 −2.7995652 hypothetical protein FLJ13154 200402 −2.7793137 hypothetical protein dJ616B8.3 815556 −2.7693 hypothetical protein FLJ10430 1055607 −2.7538365 SUMO-1 activating enzyme subunit 1 1466621 −2.7448687 ATPase, Ca++ transporting, type 2C, member 1 770675 −2.6929924 Homo sapiens cDNA: FLJ21323 fis, clone COL02374 79520 −2.6909833 RAB2, member RAS oncogene family 950355 −2.6845343 ESTs, Weakly similar to S13495 pregnancy zone protein [H. sapiens] 79710 −2.6813265 KIAA0174 gene product 2011138 −2.6569485 KIAA1036 protein 898333 −2.6509707 ESTs 878846 −2.6361347 brain protein I3 842818 −2.63282 lysyl-tRNA synthetase 1553065 −2.627227 hypothetical protein FLJ14993 136722 −2.6269431 ATPase, Na+/K+ transporting, beta 3 polypeptide 308633 −2.6261051 hypothetical protein FLJ10339 854581 −2.6159344 transcription factor 4 951241 −2.5987959 clone HQ0310 PRO0310p1 292936 −2.5940369 hypothetical protein FLJ10468 781047 −2.569753 budding uninhibited by benzimidazoles 1 (yeast homolog) 823907 −2.5587562 hypothetical protein FLJ10511 377368 −2.5495557 cell death regulator aven 292388 −2.5448438 122241 −2.539248 proteasome (prosome, macropain) subunit, beta type, 2 731223 −2.5364769 proteasome (prosome, macropain) subunit, beta type, 2 1660666 −2.534682 carbonic anhydrase VB, mitochondrial 825470 −2.530053 topoisomerase (DNA) II alpha (170 kD) 1472719 −2.526978 SMT3 (suppressor of mif two 3, yeast) homolog 1 869375 −2.5249164 isocitrate dehydrogenase 2 (NADP+), mitochondrial 302292 −2.5097213 exostoses (multiple) 2 1175007 −2.4998247 tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain 1422338 −2.488461 ribonucleotide reductase M2 polypeptide 2014034 −2.4843808 methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase 50884 −2.4377483 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 1474424 −2.4345879 Homo sapiens cDNA FLJ12758 fis, clone NT2RP2001328 753285 −2.4324065 glycogenin 700792 −2.4311609 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 259950 −2.4310983 hypothetical protein FLJ14991 610326 −2.4214624 284004 −2.4185183 ESTs 756595 −2.3963227 S100 calcium-binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11)) 128711 −2.3891503 anillin (Drosophila Scraps homolog), actin binding protein 1582738 −2.3882015 uncharacterized bone marrow protein BM040 1915867 −2.3829702 Homo sapiens cDNA: FLJ21086 fis, clone CAS03272 754582 −2.3765311 ecotropic viral integration site 2A 462961 −2.3685047 dihydrofolate reductase 705064 −2.3682586 transforming, acidic coiled-coil containing protein 3 1553696 −2.3605995 vanin 1 129294 −2.3507956 ESTs 809588 −2.3342142 gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) 1909526 −2.333814 ESTs, Weakly similar to 2004399A chromosomal protein [H. sapiens] 815771 −2.3166739 chromosome 7 open reading frame 2 703707 −2.2865473 aspartate beta-hydroxylase 2017415 −2.2832169 centromere protein A (17 kD) 1650942 −2.2797717 Human proteinase activated receptor-2 mRNA, 3′UTR 645079 −2.2761946 3′(2′), 5′-bisphosphate nucleotidase 1 133213 −2.2753496 fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid- specific) 788566 −2.2752004 Purkinje cell protein 4 2009574 −2.2646007 T brachyury (mouse) homolog 1897302 −2.2563379 serine/threonine kinase 17b (apoptosis-inducing) 78869 −2.2539078 cell membrane glycoprotein, 110000M(r) (surface antigen) 590759 −2.2513499 sterol-C4-methyl oxidase-like 785368 −2.2489394 PDZ-binding kinase; T-cell originated protein kinase 1714689 −2.2489064 ESTs 795197 −2.2481741 ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5) 781472 −2.2390098 Tax1 (human T-cell leukemia virus type I) binding protein 1 1469966 −2.2375228 delta (Drosophila)-like 3 1587847 −2.2354975 minichromosome maintenance deficient (mis5, S. pombe) 6 209066 −2.2325695 1035796 −2.2308926 ESTs 233464 −2.2280935 epithelial V-like antigen 1 753320 −2.2104141 hypothetical protein FLJ20533 486626 −2.2095389 ESTs 1505038 −2.2060272 hypothetical protein FLJ20171 503851 −2.1992378 nuclear receptor co-repressor/HDAC3 complex subunit 503671 −2.1939286 Homo sapiens cDNA FLJ14368 fis, clone HEMBA1001122 610326 −2.1885269 712139 −2.1839319 ADP-ribosylation factor-like 7 471196 −2.1797647 integral membrane protein 3 753215 −2.1781545 guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 183556 −2.1734918 gap junction protein, alpha 4, 37 kD (connexin 37) 809557 −2.1667294 minichromosome maintenance deficient (S. cerevisiae) 3 610326 −2.1633594 hypothetical protein MGC12992 1600239 −2.1602202 HSPC037 protein 1049291 −2.1593791 olfactory receptor, family 7, subfamily E, member 47 pseudogene 839682 −2.1475459 ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13) 950897 −2.1419057 Homo sapiens mRNA; cDNA DKFZp586G1922 (from clone DKFZp586G1922) 712577 −2.1411578 holocytochrome c synthase (cytochrome c heme-lyase) 824524 −2.1400285 UDP-galactose transporter related 241348 −2.1301572 prenylcysteine lyase 823930 −2.1259223 actin related protein 2/3 complex, subunit 1A (41 kD) 150314 −2.1206632 lysophospholipase I 795498 −2.1190094 putative transmembrane protein 82710 −2.1184513 glutathione S-transferase A2 1869201 −2.1135906 hypothetical protein MGC2745 1694526 −2.1126121 hypothetical protein FLJ11029 823598 −2.1072985 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 214162 −2.1065234 metallothionein 1H 811590 −2.1050783 hypothetical protein FLJ11100 796904 −2.1050163 pleiomorphic adenoma gene-like 1 1517595 −2.0965219 KIAA0175 gene product 282428 −2.0954489 ESTs, Weakly similar to A46010 X-linked retinopathy protein [H. sapiens] 1883219 −2.0949091 ESTs 746229 −2.0906355 mitogen-activated protein kinase kinase kinase kinase 4 610326 −2.0896786 hypothetical protein MGC12992 1632225 −2.0828168 ESTs 743810 −2.0796998 hypothetical protein MGC2577 1416055 −2.0725881 extra spindle poles, S. cerevisiae, homolog of 1626297 −2.0656173 hypothetical protein FLJ20509 852829 −2.0608067 karyopherin alpha 3 (importin alpha 4) 840511 −2.0554449 vimentin 278504 −2.0519206 neurochondrin 1534700 −2.0506628 KIAA0830 protein 812276 −2.0458249 synuclein, alpha (non A4 component of amyloid precursor) 306841 −2.0449642 T cell receptor beta locus 3172883 −2.0437672 ESTs, Weakly similar to 1709359A dopamine D4 receptor [H. sapiens] 624627 −2.0409259 ribonucleotide reductase M2 polypeptide 486179 −2.0380168 Homo sapiens cDNA FLJ10205 fis, clone HEMBA1004954 376316 −2.0218598 wee1+ (S. pombe) homolog 37671 −2.0190035 hypothetical protein FLJ21610 629944 −2.0166696 myosin VB 713158 −2.0133834 ESTs 504308 −2.0067977 hypothetical protein FLJ10540 1605426 −1.9957389 hypothetical protein FLJ13352 810711 −1.9920785 stearoyl-CoA desaturase (delta-9-desaturase) 263790 −1.9904129 isocitrate dehydrogenase 3 (NAD+) alpha 549349 −1.9893582 hypothetical protein PRO1068 109221 −1.9879196 KIAA0286 protein 51773 −1.9875155 hypothetical protein MGC3077

Example X Crossvalidation

The following table shows the results of crossvalidation analysis (as described in Example I above) of various pair-wise comparisons. The two members of the pairwise comparison are indicated as “Class 1” and “Class 2” with the number of samples analyzed indicated under “N”. The number of genes used to predict is indicated, along with the accuracy (in percent) for each combination. “FP” and “FN” refer to “false positive” and “false negative”, respectively, as incorrectly identified for each of the two classes. Class Class Class 1 Class 2 1 2 Name N Name N Genes Accuracy FP FN FP FN Normal 28 Abnormal 57 850 99 0 1 1 0 Normal 28 ADH 7 600 100 0 0 0 0 Normal 28 DCIS 28 1300 100 0 0 0 0 ADH 7 DCIS 28 350 97 0 1 1 0 ADH 7 DCIS 28 10 97 0 1 1 0 N + 36 DCIS + IDC 49 400 98 1 1 1 1 ADH DCIS-I 7 DCIS-III 9 300 100 0 0 0 0 IDC-I 4 IDC-III 8 300 100 0 0 0 0

REFERENCES

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All references cited herein, including patents, patent applications, and publications, are hereby incorporated by reference in their entireties, whether previously specifically incorporated or not.

Having now fully described this invention, it will be appreciated by those skilled in the art that the same can be performed within a wide range of equivalent parameters, concentrations, and conditions without departing from the spirit and scope of the invention and without undue experimentation.

While this invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications. This application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth. 

1. A method to determine the breast cancer stage of a ductal lavage or fine needle aspiration sample from a subject comprising assaying said sample for expression of 5 or more of the genes in any one of Tables 2-5, which genes are correlated with one or more stages of breast cancer, and determining the breast cancer stage of said sample based on the level of expression of said genes.
 2. The method of claim 1 wherein said assaying comprises preparing mRNA from said sample.
 3. The method of claim 1 wherein said mRNA is amplified.
 4. The method of claim 1 wherein said assaying comprises detecting expression by use of an array.
 5. The method of claim 1 wherein said assaying comprises detecting expression by use of a microarray comprising polynucleotides which hybridize to said genes.
 6. The method of claim 1 wherein said expression of 5 or more genes is correlated with ADH, DCIS, and/or IDC.
 7. The method of claim 1 wherein said one or more genes are correlated with normal or abnormal cells.
 8. The method of claim 5 wherein said array comprises polynucleotides which hybridize to more than 5 of the genes in any one of Tables 2-5.
 9. The method of claim 1 wherein said subject is human.
 10. The method of claim 1 wherein said subject is afflicted with, or suspected of having, breast cancer.
 11. The method of claim 5 wherein said array comprises polynucleotides which hybridize to more than five of the genes in Table
 2. 12. The method of claim 5 wherein said array comprises polynucleotides which hybridize to more than five of the genes in Table
 3. 13. The method of claim 5 wherein said array comprises polynucleotides which hybridize to more than five of the genes in Table
 4. 14. The method of claim 5 wherein said array comprises polynucleotides which hybridize to more than five of the genes in Table
 5. 15. The method of claim 1 wherein said sample is a microdissected sample.
 16. The method of claim 15 wherein said sample is microdissected via laser capture microdissection.
 17. The method of claim 6 wherein said one or more genes are correlated with ADH or correlated with DCIS or correlated with IDC.
 18. The method of claim 6 wherein said assaying comprises preparing mRNA from said sample and optionally amplifying said mRNA.
 19. The method of claim 6 wherein said assaying comprises detecting expression by use of an array.
 20. The method of claim 6 wherein said subject is human, optionally afflicted with, or suspected of having, breast cancer. 